Most of the homebrew programs can be updated by installing the new version on top of the older ones, but is not a rule and there is something to consider about this
Personally the way i see it is:
1) Finding bugs and betatesting a single version of a program is a thing (and that thing could take lot of time)
2) But finding incompatibilities with previous versions of the program is a different thing (and i guess not much devs does it)
3) And finding incompatibilities with other programs is another different thing (and i guess not much devs does it)
The problem in case (2) is most hombrews apps uses a settings file, or files that are generated by the program. If for some reason the format of that files changes (because the developer implemented new features or decided to do some changes in how that files works) it could happen that the program boots with some problem, or even that refuses to boot
This is not usual to happen, because the devs takes care to dont step into incompatibilities, also because they knows when that files could cause some problem
But you know... this is a homebrew scene, the bugs happens, and as mentioning before this small incompatibilities could be hard track, mostly because the time the devs have for debuging and betatesting is limited, and the priority is to do it with the latest version of the program only (and forget about the previous versions that have less features)
The problem (3) is way harder to track it, the compatibility in between programs is only tested if the other programs is a "must have", but this is something subjetive and a personal oppinion
Personally i prefer to uninstall the previous version of the program before installing the new, but is just a preventive meassure "just in case", also because i consider this kind of incompatibilities cant be considered a mistake of the developer, is just something that could happen eventually and we should get used to it
Also, if at some point your program have some weird (black magic) behaviour, the first thing you need to do is to unsintall it (to clean up the files in the installation path/s) and install it again