If I may ask, why wouldn't you recommend it ?
I've always done the approach to update apps / VNs on top of their exisiting apk, and it almost always has worked without issues. Should I stop doing so ?
Mobile apps are designed as complete packages, not as incremental updates. I would never install an application on top of an older version, as you don't know which files are kept, and which files are replaced. The creator must really be vigilant when creating a new installer, and mistakes happen. Obviously, we don't reinstall windows whenever there's a new update - which is every 5 minutes these days, but that's created differently. To give you another example; When you update your GPU driver, you would prefer the "clean install" option, to make sure all relevant files are updated, and no bad mix of old and new files exist.
Since I can't be sure.. I'll always remove the app, before installing a new version.
Often, removing it will not removed the save game folder, but sometimes it will.
That's my opinion anyway :)