Yes there are differing opinions over pine but I have used it for years with many animals. I don't use it for my guinea pigs or rats because I always end up with most of it all over the floor. Though I used for my first two rats and they lived for almost 4 years which is old for rats.
I think I read somewhere to smell it and if it smells strongly, don't use it. But I could be wrong.
Personally I can't see a proplem with lids if there needed. A lid made from cube grids isn't goning to affect the ventilation. Didn't bother with a lid for mine as I have no reason for one.