If you play all your games with a controller absolutely, the main situations where you wouldn't want to use v-sync is for games that benefit from unlocked frame rates and when using a mouse, for example in Counter Strike where you want the most precision mouse aim possible, the higher your frame rate the less input latency there is, or RTS's, since v-sync is intentionally delaying what is shown on the screen in order to sync mouse input lag increases dramatically (some RTS's separate the mouse cursor from the render and are immune to this issue).
You mentioned emulation but it's worth noting many emulators use custom video plugins that don't obey Nvidia overrides, however pretty much all console games are frame rate locked so it's not something you need to worry about.
Low latency mode can have drawbacks, if you've got system resources to spare no problem but the mode utilises your CPU to promote and discard frames in a manner that promotes responsiveness, from what i understand, so using it in a game that is demanding a lot from your CPU might actually create more input lag or a stuttery image as frames are discarded, similarly if a game isn't pushing your hardware you might not see a benefit, just a higher CPU cost, Overwatch players report that it actually creates input lag so use it on a case by case basis or if you're trying to resolve an input lag issue.
I use v-sync for pretty much every game except where noted above, i only have a 60hz monitor so i only use higher frame rates for competitive shooters.
Edit: I didn't know what Citra was when i posted, i guess in this case it is obeying control panel settings, many people have more luck using Nvidia's v-sync options compared to those built into games, or in this case an emulator.
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