Yeah, mothballing has never been as prevalent or as useful as romantics make it seem.
That's exactly why it would make a workable mechanic if introduced into the game; because it would be difficult, time-consuming and have serious strategic trade-offs. If it was easy, simple, and cheap, all it would do is effectively balloon the number of ships an empire of X size could muster; and NPRs would do the same, leading to effectively no difference except more tonnage.
The real hurdle is that even realistic mothball rules - where it takes a month or more of intensive work at a dockyard to return a ship to service - has not nearly as much strategic trade-off as it does in real life due to how Aurora's FTL mechanics work - warp point blockades make your own borders very, very defendable. The attacker would have an advantage when he un-mothballs his entire fleet and the opponent hasn't unmothballed theirs until they're attacked, so even assuming NPR AI is improved to be more aggressive and calculated when waging war, there will just be a strong first-mover advantage to contend with.
It's not that the mechanic can't be implemented - in a sensible way, even. It's just that fundamental design choices of Aurora would render it mostly moot.
There are RP reasons to want this mechanic, but that's what we have SpaceMaster for. Gift yourself requisite MSP (or minerals for such) to maintain the # of ships you want (or turn maintenance on and off in the options as needed) then make your "mothballed" ships enter overhaul then immediately abandon it to get penalties simulating the unmothballing process, is one suggestion.
A lot of feature requests are actually enhanced SpaceMaster option requests in disguise, I feel.