I have been thinking a bit and cannot , in fact think of any other instances with
huge damage (other than in alternate timelines, so yes, they don't count). Caretaker perhaps? We don't know how badly the ship itself was damaged but with several dead on-screen (and probably much more off-screen as well) I'd imagine the ship to be badly bruised , too.
I would also expect the ship to be at least moderately damaged (perhaps requiring somewhat more than a week of repairs) in episodes such as
basics where there were battles and explosions both within and around the ship several times.
Still, there are a lot of instances with moderate damage, and I'd think they add up. Especially in the first 2 years, when we're supposed to believe they are mostly trying to evade the Kazon and the Vidians. You can patch up your engine room after a Kazon attact that damaged your ship so badly you can only do warp 2, but I would expect there are only so many times you can do so, before you really would need a major overhaul, which we see them give Voyager, well, once, in year 7, if I'm not mistaken. If only they had known they'd be home a mere 16 episodes later they could have kept the counter at 0, and it would have looked even nicer on Janeway's resume....
As for the shuttles, I have to apologise, as I misworded there. I didn't mean to say they were churning them out in fleets at the time, but that they eventually had to build a fleet's worth of them, over the series run. 10 shuttles lost is only counting those we're absolutely sure about, the tally is probably significantly higher. According to the detailed table given in
http://www.ex-astris-scientia.org/inconsistencies/inconsistencies-voy.htm , 10 were definitively lost, another 7 probably lost, and an additonal 8 badly damaged. Picking a number in the middle range would average in building 2 shuttles per year and a major overhaul for a third. I'm positive that can be done in terms of manpower (seeing as they built the more complex Delta Flyer in a week or so), but still I think the resource management officer (whoever that may be) isn't too thrilled about it, strained as the supplies are -- but yes, shuttles are a necessity.