As long as the hydrometer doesn't touch anything, it will not be affected by what is in the tube with it. I wouldn't worry about the foam padding, but it wouldn't hurt to get it out if you can. Btw, I sample and take hydrometer readings with my wine thief - a fantastic device that makes sampling really easy and is just about perfect for my hydrometer.
As far as your explosion, sorry to hear it. Where did store the fermenter before the kitchen? If it was someplace considerably cooler, that may account for the stop and restart of the fermentation.