Do ships altered through this mod still get targeted by hull restoration? If so, would there be a way to prevent that?
They will still be affected by Hull Restoration; this mod doesn't do anything to prevent it from quickly restoring the D-Mods you just added/bought to your ships. However, there is a tag that completely prevents any restoration at all (whether by dockyard restoration or by Hull Restoration), which...
Story Spoiler!
...certain [REDACTED] ships related to a vanilla side quest do have...
...so it is something I could possibly implement in the future. No guarantees about that, however!
As for Hull Restoration itself, changing vanilla skill mechanics is outside this mod's scope, though, of course, there may be other mods out there that do something like this.