Never had any problems with updates. I’m not even sure what issues you’d have… Softaculous is totally fine, and if you don’t like the bloat… then uninstall and do it manually.
Just a head up, if you’re asking this question I’m assume you don’t have a lot of experience, but WordPress sites are very easy targets for attackers when you start installing plugins and don’t keep them up to date. Make sure whatever you do you’re on top of the maintenance of it.