It just seems like an artificial system designed to make the player micromanage things. If the AI used it I would be more inclined to keep it on, but if the AI just ignores it why should I bother to take all the time micromanaging it? I can guess why they ignore it - Steve probably didn't want to go through the trouble of programming them to check maintenance clocks and send ships back for overhaul and such. And handling disabled ships that run out of supplies and lose their engines or something.
Theres another thing the AI ignores too - shipyard refitting. They never actually set shipyards to build certain ships. They just pop out ships of any type as long as the size fits. Looking at them with designer mode I even caught them building military ships in commercial shipyards. The inability to clear a shipyard of the ship its going to build has always been a pet peeve of mine - in some cases it's easier to build a new shipyard and expand it than expand an existing small shipyard and then go through an expensive process of refitting it to the larger design - especially if the larger design is very expensive.
I kinda wish there was an intermediate maintenance option that made ships have a set rate of failure not based on an overhaul clock, and just require resupply with maintenance supplies every so often. That way resupplying a fleet of defense bases would be as simple as sending a supply ship every few years, instead of having to send tugs and give a bunch of orders to tow them back and forth. Maintenance facilities could be changed so that instead of keeping a ship at 0 clock or rewinding the clock they would reduce the failure rate of ships in orbit and take the supplies from the planet so you don't have to give the order for the ships to resupply constantly. With a system like this I'd even like to see civilian ships require maintenance, maybe at a reduced failure rate so they can go further between resupply and don't require as many engineering sections. It'd make more sense to have civilian and military parts instead of the whole ship, so you could still use civilian engines on a military ship for reduced maintenance cost if you wanted to - and putting one military part on a civ ship (like, say, grav sensors) wouldn't suddenly make your commercial engine start breaking down.
The minerals used aren't really enough to be concerned about unless you're running out, and there are simple ways to completely bypass the whole thing (build a PDC with docks, land ships - presto, in overhaul but ready to be launched at any minute. Bonus: no maintenance facilities required, no mineral losses, no wealth cost, quick repairs to any ship landing at the cost of MSP). I've gotten to where I just transport hangar PDCs out to my colonies and assemble them, and land my defense fleet in them - so im practically ignoring overhauls already.
I haven't really played a game that lasted long enough to get too upset over it; the only ships that spend much time away from Sol and the adjacent colonies are my survey ships (partly because I keep trying to make jump tenders to help with my battle fleet's force projection and making mistakes, heh. I should just build a jump-capable warship at this point.)
That said from a purely theoretical standpoint I like having maintenance on. For some classes of ships it gives a design consideration (namely that commercial engines require no maintenance). There are some strategic considerations as well since it provides another upper limit on how long a fleet can be out (assuming they have a tanker), at least without having a dedicated mobile maintenance platform (which is a ship type I like the idea of, although it looks like Maintenance Modules require 5000 tons of repair-er ship to 200 tons of repair-ee ship which looks like it gets kind of ridiculous fast). Brand new colonies also need infrastructure (as in maintenance facilities, not actual in-game infrastructure) to properly support a defensive fleet, which takes time or resources. I also like the idea of ships being caught pants down while in overhaul, requiring you to make sure all your cruisers aren't getting the metaphorical spa treatment when invaders come knocking. Also, the need to cycle ships on sentry-type posts.
I do agree it's a shame the AI is a cheating bastard with it, and I'm glad it's an option so people who don't like the micromanagement don't have to deal with it if they don't want to. I just like that it adds a few more relevant decisions to the game and enjoy the little injection of realism.
Those are the same reasons I've kept it on so long. I do like the strategic implications, and even if I play with it off I'll still be designing most of my ships the same way as I always have with maintenance supplies for repairs and such. Supporting a proper defense fleet on a world requires more than just a maintenance facility anyway. You need ordnance, fuel, maintenance supplies for repairs, maybe a shipyard to do armor repair (or a hangar PDC, heh).