1) 5.1.8 Hitler's restrictions. Does it specifically refer to CV only or it should also refer to aircraft carriers (CV+CVE)?
CV only. During the period of this game, British CVEs did not carry strike aircraft and were no threat to Tirpitz.
2) the only place I can see that the torpedo boats can attack only from Torpedo section of battle display is is surface combat EoP.
3) in the player aid I can sea that 9.3.2 only applies to campaign. Is it correct?
No; this is an artifact from older rules that I failed to delete. No one ever noticed before! If a convoy disperses early in a fortnight, the Germans may be able to destroy lots of the dispersed MVs before the convoy can reform. In an Operation scenario, this is a potential game-breaker, as the Allies won't have time to recover. So originally I limited this possibility to the Campaign scenario, but changed my mind to simplify matters and because the circumstances have to be just right (or just wrong, if you're an Allied player!) for this to happen.
4) 12.3 prior to day 12. What does it mean? Does it mean that by the first turn of 12 day the fee should be paid?
It's not a fee unless the Axis player tarries. If the Axis convoy fails to arrive in Kirkenes by the end of Day 11 PM, the Allied player scores the indicated VPs.
5) 12.8 what is a minelaying objective hex?
A hex with a German Minelaying Objective symbol.
6) 12.12 should we deduct the 5VP?
If you send a CB into the Kara Sea, you must deduct 5 VPs once during the operation.