There is no reason to assume Dragon Maid S2 won't come out. It wasn't even confirmed that it was made by KyoAni in the first place, but either way, it's not like all their staff died...
The fire did more than kill people; the studio was the main pipeline of their workflow and housed most of their keyframes. Anything they were working on can probably be assumed to be cancelled. ...But, yes, it's unclear if KyoAni was working on MaiDragon S2 in the first place, and I personally doubt it
Considering they made a statement that their movies will come out without delay, there must have been some precautions at the very least. These days you don't keep all this stuff in one place. I mean it's kind of a given you make safety copies.
It depends on, among other things, where their servers were housed. Some stuff might have been kept on-site and others elsewhere. But also a lot of the actual animators were killed or seriously injured, so they've taken a huge hit to their talent pool. It's not just the directors, but all sorts of people involved with those projects, and now they're either gone or out of commission for months at minimum given how nasty burn injuries can be.
I can see them pushing for completion of the big ticket projects like movies with their remaining staff (people who worked off-site, at other locations, etc.), but there's gonna be a price that'll likely be paid with lower-margin TV work being delayed or cancelled.