Your experience may depend on which distro you use and how you install things. If you use a distro with a stable upgrade path such as Debian and stick to system packages there should be almost no issues with upgrades. If you use external installers or install from source you may experience issues depending on how the installer works.
For anything complex these days I’d recommend going with containers that way the application and the OS can be upgraded independently. It also makes producing a working copy of your production system for testing a trivial task.