It's really not a insurmountable issue for developers to resolve in future add on updates.
First, the new schema manager add on devs should be using his resiliency built in to cope with certain scenarios such as conflicting database tables and columns.
Second, the developer can write code in their updated add on to detect this and even repatriate the data from a now uninstalled add on if necessary (or just remove it).
Ultimately the advice will be to uninstall an add on before uogrwding if you know it will never be used. If you end up having to uninstall a legacy add on later, there's plenty of measures in place to cleanly and transparently resolve it.
That only makes sense if a) you know you don't need the add on or, b) you know the add on most likely won't be upgraded in the future. Otherwise, just leave it and either wait until an update is available or eventually remove the add on.