slightly morbid, but for cycling purposes, yes you probably could have left them in. The hermits would likely have made quick work of them though.
by unprocessed you mean uncooked, right? just making sure you're going to get the right thing.
as far as closing the canopy... I must have missed the first time you said you had a wet-dry. The part of the wet-dry that the water trickles over the bio-balls should actualy give you plenty of gas exchange. The sudden ph
drop was likely then just part of the many fluctuations your water levels will make over the course of the cycle. I wouldn't be too concerned over the ph
until towards the end of the cycle. be sure to get that shrimp in there soon. If the tank goes too long without some supply of ammonia, the bacteria that processes it will die off and you'll have to start your cycle over again.