I dunno about you, but I make my wealth off civilian shipping lines.  

Judicious use of terraforming ensures that demand for infrastructure never falls below supply.  (ie. I do not terraform colonies below 2 cost until they hit 400m or so)  This ensures that infrastructure produced by terraformed high population worlds always have a market in developing colonies.  

Not to mention, researching the wealth tech improves trade goods as well.  Combined with affordable freighter and colony ship designs, all I have to do is plonk down a colony designation and 1 freighter-ful of infrastructure and the civvies do the rest.  
Moving industry is also a piece of cake.  I placed an order to move 100 maintenance facilities to a forward base and it got there in about six months...

Heck, by year 30, I abandoned my game because it was getting so slow with all the civilian traffic!  More than three hundred one thousand ships spread over 8 shipping lines, all busy like bees shuttling stuff between my capitol (1b), research world (~400m) and manufacturing center (600-700m), as well as roughly 20 satellite colonies (10-100m).  
Shipping line tax income was around twice my tax base.  

I'm wondering how you have enough people to run a place like that, good god...

There are ridiculous gobs of minerals everywhere, it will literally not be possible to exhaust them all, though finding good sites to mine can be difficult. In one game I have 62 ships in the 10k to 20k range parked over my capitol sucking down a lot of resources(12k of all types per year), but there are 4 thousand mines spread out over 5-6 mining colonies producing minerals for my capitol so despite having 3 full taskforces, I have quite the reserve of minerals and the ability to crank out ships should it become necessary. The mineral I have the least of is neutronium, at 128k in the stockpile, and the mineral I have the most of is Duranium with 1.693M.

What I lack at this level is cash, quite simply because I have enough resources to build way too much with 3000 construction factories, 400 labs, and 13 shipyards with 42 slipways between them.

If I remember correctly from when I tried it out a while back, in a game with maintainance switchd off, even for ships that have high accrued maintainance clocks, overhaul orders don't show up in the available orders unless you select the 'don't filter orders' option. If then given the overhaul order, the ship will get stuck in permenant overhaul state with the clock never reducing and being unable to recieve any orders. The only way to get them out of that state was to cancel all orders for the ship and then put the ship under repair at a shipyard.

Running a game with maintenance turned off currently, and the overhaul option is there. It's just ordering ships to be overhauled does nothing but put them into the overhaul state. Doesn't reduce timers at all, and requires "abandon overhaul" order to get to normal operation.

I found this out after forgetting that i had maintenance turned off; i was in a habit of ordering overhauls whenever a fleet's duty finished.

Have you considered that it might be time to retire your old ships?

I've never had a problem with maintenance. I tend to give most ships generous maintenance spaces, and they only usually last 10 - 20 years before being replaced by newer generations of ship. On one design made in a critical duranium shortage for one faction, I built a military freighter design with barely enough maintenance spaces for one failure (the faction only had a fairly small naval shipyard at the time, but needed to get some automines offworld ASAP), and just ordered them to resupply every cargo-trip cycle. When they were doing nothing in orbit of the planet, set conditional orders to resupply below 20%. I very rarely overhaul my ships at all.

Did you press Save?

You can change everything else midgame I don't see why maint would be different.

I don't know if checking the "no Maint" button during the game changes anything, but if checked at the beginning your clocks keep ticking but no failures ever occur.  You can roleplay the need for maint and such or you can just ignore it and build huge ships with little engineering spaces and never worry they might break.

Mark