Hi, When a fleet commander has txt about friendly ships does that mean every ship from his faction EXCEPT the one he's on get the benefit. E.G if I put Motti on an ISD will it get the 3 extra hull points or not?

Yes, he does. "Friendly" is every ship in the same fleet, including the flagship.

from the RRG:

"A ship or squadron is friendly to itself and can be targeted by an effect that species a friendly target unless it explicitly species “another” ship or squadron."