Yes - EC261 will still be payable.
Am I reading this right? You chose to go to a hotel rather that just go home for the evening?
Regarding T1 security. Generally, you go through security upstairs - however, they sometimes direct people downstairs to the Jet2 security point. It's well worth paying £5 for the Fast Track, as this is always upstairs, and yo'd be through in about 5 minutes.
PS.... good luck with the B787 in Y. I've never done it myself, but it doesn't get the best reviews!