Does this 3 pip cancel out any attack that could be made when Vader is activated again? So he couldn't attack either time?

Vader cannot attack as long as I am a Jedi is active, ie the entire round. So probably not the best idea to activate Vader twice unless you have a really good plan to use the extra action without attacking ;-).

None of his force powers (except saber throw) count as attacks. So if you have a good reason to use them multiple times, like choking a couple minis or pushing a couple units around off of objectives or into vulnerable positions, it might be worth triggering his Implacable ability.