If you are querying if you can give tank hunters to an annihilation barge then yes, you can. Nemesor allows you to gift it to any of your units... so as long as its a unit it counts. I've used it to good effect on an annihilation barge too - as you point out, the twin link to hit makes a big difference when it comes to maximising the advantage to damage rolls.
One thing I found out though, is that tank hunters has very specific wording which stops it being used in full against buildings with an AV.
I do have to agree with your target acquisition though - I am convinced that an annihilation barge has more chance vs flyers than a night scythe firing with skyfire... twin linking has a better chance of you getting the 6s, which tesla turns into more hits for good measure! I'm sure someone will come and mathammer me wrong... but still!
I also believe that giving the ability to an embarked unit is fine. Nemesors rule literally says you can give it to any unit in your army. The way I read it, this could even mean giving it to a unit that is currently in reserve. ie - tank hunter to a night scythe, or even counter attack to the immortals inside the night scythe currently in reserve!!
I'm also going to say that glancing vehicles to death will be a commong occurance in your games. It is the bonus necrons get for generally lacking in high strength, low AP weapons capable of instant gibbing a tank. In essence, you will likely never ever cause a tank to explode (and that's probably part of the reason for the tesla destructors "arc" rule). There are ways you can try to though - such as sending some scarabs out first to drop the AV to silly levels! (In one game I managed to drop two predators down to front armour 7 and 8!)
Now, as for the quad gun. I see no reason why you would not be able to target it. It is given a toughness and save value exactly for the reason of when it is targetted. However, I'm not so sure if it counts as a "unit" in your army for first blood. That bit is worthy of further questioning in the rules board me thinks.
One other element with the aegis that confuses me is that it says all parts must be deployed in contact with another piece - but does not clarify if this INCLUDES the gun emplacement or whether the gun can be placed separately, or simply within a certain coherency? In the absence of actually stating it can be placed anywhere I'd be inclined to say it must contact a section of wall - but even the pics of it in GW things don't have it like that... Personally I'm happy to say it has to be within 2" of a section of wall (mostly to stop someone deciding to deploy the gun in a completely separate and secondarily advantageous position!)
As for the crypteks - their use really depends on their set up.
