1-In theory they have a problem with the code with that, since EBBs/BB6s have some special atributes that make unable to put them on HQ. But i never completly understood that since the EBBs0.5 were tradeable in the past and they were allowed to be put on HQ.
2-I never had clear if that is just an unfixed nosense or it is something deliberated done for preventing certain kind of things. It's just like the credit account counter overflow issue, you can't be sure if they are deliberated unfixed mistakes or not.
3-When the olive trading was active i remember to made one trade but i made the mistake of not letting enough space for all the crew. Anyways they were put on my account and i surpased the 50 sailors limit by 4 or 5. So i guess there is no problem on rising that limit, but HQ pages are items and give them $$.
Send ticket if you want to know official and clear (lol) answers.