Other than a free oil change and recalls, and a tire change (about $150 for tire plus service charge) on my 2013 Zero S, I haven't taken any motorcycles in for service in a long time. I did buy a maintenance contract on my 2011 Gixxer 1000 that cost $1500. I put 11,000 miles on the bike in about 11 months and the maintenance service transferred for an additional 2 years so that was built into the trade-in when I sold the bike, so I'm not sure what I really paid for that. I did it to have the valve adjustment, but never got to that mileage so all I really got for my $1500 was 4 oil and filter changes 3 out of 4 new spark plugs (the 4th one was going to wait for the valve check) and an air filter, chain adjustments and other minor adjustments. I know how to all routine maintenance including valve checks which is all my bikes have needed. Plus I like to work on them. I have just under 10,000 miles on my Zero and haven't had any issues other than an occasional rogue warning light coming on, but that was before the firmware recall 5,000 miles ago or so. I did own a 2011 Zero S and the brushes went out on that bike under warranty, but that bike was very light and I pushed and coasted home and since my dealer is only 4 miles from my home, he picked up the broken bike from my home. Rather than deal with putting another brushed motor in the bike, I traded it in, after a year or so.
It's probably hard to figure maintenance costs on a Zero, but I suspect the maintenance costs after 2 years will be higher than most ICE bikes, but that's just a guess. If you have to replace chargers, motors, battery cells, it's going to be many hundreds of dollars and significant down time unless you can diagnose and work on the bike yourself. Feast or famine, I suppose. There is one other issue to consider. That Ninja 300 I mentioned has a very good resale value. I don't think the resale value on Zeros is very good, so that's perhaps a negative. Like you say, when they work they are fantastic, but when they don't it's a downer. I will probably just ride mine until it breaks or until I want to trade in for another Zero or some other motorcycle. Personally, I doubt I would put $1000 into fixing my broken Zero once it's out of warranty in a couple months. I'd just trade it for whatever I could get, be done with it and hop on another bike. I have always thought of Zeros as expensive toys that will cost lots of money to run.
OOps. Just remembered I did have one minor issue on my Zero. A solenoid went out so some of the lights didn't work. The dealer fixed that promptly by picking up the bike and returning it to me, which was very easy for me and why I forget I even had the problem.