Capping them is a good idea as long as you remember to uncap when you get to your destination. If you forget to uncap i could imagine you will collapse the tank if the air cant replace the water you are using. (if the pump is strong enough to keep sucking)
As far as siphoning the water through the vent tubes. If you are able to siphon the water out, then the vent tube is going in too deep into the tank. It should be connected right at the top so not able to siphon.
I was thinking of using those little air bed plugs or old beach ball stoppers.
2017 Eagle 324 BHTS pulled by 2014 Ram 3500 CC CTD Laramie. Air bags.