I did not find anywhere in the rules or FAQ, what exactly happen when i drop conner net token and it overlaps base of two or more ships ? Detonates obviously but does the effect of one damage and two ion tokens suffers just one ship or all of them that was overlap by the conner net token ?

as far as I remember you choose which 1 ship it effects

Correct, if two or more ships are overlapped by one bomb token being dropped that detonates on overlap, the dropper of the bomb chooses one ship to be affected.

It's in the rules under "Bombs".