Hepburn is poorly supported in some input methods, like on Windows. If you want to type kōen or whatever, you really have to work for that ō. It's better now on mobile devices and MacOS (what I'm using now): I just long-pressed o and picked ō from a pop-up.
That's one aspect I really love about macOS. I'm from a small country so nearly no one makes hardware with our exact layout, but with macOS I can always just long press to fill in the gaps. I just wish all apps used native inputs, not some weird half-baked solution they built themselves.
I rarely miss Linux, but I liked being able to have compose keys, most of which were very logical and fast to type. Now on MacOS, I either have to know the option (alt) combination or long press, which makes my writing with accents way slower.
My favorite Linux layout was US International + AltGr dead keys. Basically a US keyboard, but if you want an accented character, just press the AltGr+Accent key, then the letter.
If you frequently write the same characters, it's straightforward to create your own keyboard layout that matches your usage, using https://software.sil.org/ukelele/
Same with image viewers on the web. Google, twitter, imgur, and others seem hell bent on making the shittiest possible zoom and pan implementations to look at images.
What's the best way to type Japanese on Windows? (I have a QWERTY keyboard)
On mobile I just switch to the hiragana keyboard, but that obviously isn't a sane option on desktop unless I'm clicking all the characters with a mouse?
This is a good question. I have seen a wide variety over the years from native Japanese speakers. Some use the 1990s-style kana keyboard. Some use romaji input where real-time software (called an IME) automatically suggests conversion to the final Japanese word (katakana/hiragana/kanji, etc.). On a mobile phone there is usually an option to do 1990s feature phone style kana input, where the 12 key input is shown, and you press one key as many times as necessary to rotate to the correct kana that you wish to input. You can see young girls with frighteningly long fingers nails jamming away -- chatting with their friends via mobile text (Line, SMS, etc.). Their "touch memory" (and sensitivity) must be jaw-droppingly good -- like a professional drummer or something similar.
Native Cantonese speakers in Hongkong have similarly diverse input methods. I've even seen tiny digital draw pads at the public library. It is pretty exciting (to me!) to watch an elderly person furiously scribbling away on the pad, inputting traditional Chinese charaters to search something on the Internet or in the media catalog. I think it is very cool that public library makes a strong effort to empower all types of users.
Using the example from the top-level comment, you would install an IME, switch to hiragana mode, start typing "kouen" and convert to kanji when you see the right suggestion.
It might sound complicated at first, but you can do it pretty fast once you get used to it.
MS-IME or Google Japanese Input. (whatever)-Mozc on Linux. Use "IME On" mode for Japanese, "IME Off" mode for alphanumeric text inbetween.
"shio ha natoriumu[Space][Return][ImeOff](Na)[ImeOn] to enso[Space][Return][ImeOff](Cl)[ImeOn] kara dekite imasu[Return]"
-> "しおはなとりうむ(Na)とえんそ(Cl)からできています"
-> "塩はナトリウム(Na)と塩素(Cl)からできています"
(NOTE: spaces added for legibility)
Most Japanese users use this "romaji" input - which is more vibe heuristics based and not highly consistent with existing romanizations hence the change. Some use "kana" with full 51 Hiragana symbols on JIS keyboard(with ろ/backslash/underscore key to left of RShift, which makes it incompatible with ISO). I think "most people don't do this anymore" remarks refer to the fact that everyone's on the phone, and uses the "flick" input.
As others have said, people prefer different ways. My wife (Japanese) writes on Windows (Japanese edition) in romaji, and she's very fast. But she also says that in fact most Japanese (at least of her generation) don't write that way (they presumably use those small kana letters on Japanese-variant keyboards). As a non-native I also write the way she does, though I'm on Linux. I'm not sure why my wife writes using romaji, I should ask.. she wasn't an English speaker or anything, so why that worked for her I don't know.
When it comes to input "best" is highly subjective, but with that said: Just adding Japanese support in the system language settings is fine.
Standard Qwerty keyboards are well supported, you'll need to either check the key shortcut to switch between inputs or do it with the mouse if it's infrequent enough.
People using it daily will tweak a lot more, have a straight to IME and straight out of IME key instead of the default switching pattern, potentially add more tweaks to always have half-width space and ponctuation whatever the mode they're in etc., but that's a rabbit-hole you'll be free to fall into.
BTW the reverse works well enough: Windows has a specific mode to force US ANSI on JIS layouts and still use the additional japanese keys. Kinda fun they felt the need to leave that mode in.
I don't know now, but for the longest time, Google made a much better Japanese IME for Windows than Microsoft ("Google Japanese Input"). I started using it when running into reliability issues, like disappearing kanji dictionary, or frozen switching between roman and hiragana.
Assuming Microsoft's Japanese IME is still a dumpster fire, and the Google one has not succumbed to Googleshitification, that would be a way to go.
To enable the Microsoft IME there are some rituals to go through like adding the Japanese language and then a Japanese keyboard under that. It will download some materials, like fonts and dictionaries. A reboot is typically not required, I think, unless you make Japanese the primary language.
Once you have the keyboard, LeftShift + LeftAlt chord goes among the input methods. Ctrl + CapsLock toggles hiragana/romaji input. I think these are the same for Google or MS input.
The article says the new style says that you can use either a macron or a doubled letter, but it's not clear if that's supported for keyboard input on various platforms.
But in the case of ō, you can only use a doubled letter if the underlying word is おお. If it is おう then you don't have a doubled letter you can use; you need "ou" and that's not Hepburn any more. It is "wāpuro rōmaji" (word processor romaji).
Note: bitwize is talking about how to do it on Linux. Which is the best way in my biased opinion. Perhaps not the best mapping for people who use it regularly but is awesome for those who use it irregularly. We can usually guess how to do weird diacritics without having to look it up.
(The bugs I've experienced: it doesn't properly disable itself during video games, despite claiming to do so; sometimes the popup seem to come up when I swear I didn't press the shortcut keys; rarely, the popup gets stuck on screen and needs to be Alt+F4'ed.)