Yes, it's true they arent' very effective in the end game. Maybe it they made them more powerful? And setting up pacts with other races, will a pact with Vassari and Tech give the Vassari more powerful missles. Will the Vassari receive a resource bonus as well as a trade bonus?

yeah i'm pretty sure you lose them all. You lose them one at a time if your relationship starts to fall below certain numbers.

Some of the pacts may have logical secondary abilities that would increase their utility.  The only one that comes to immediate mind is the Vasari phase jump pact: I'm sure many people would enjoy it if it allowed the pact-partner to use the Vasari member's phase lanes... but this may be difficult to code and would probably also justify swapping the phase pact's required % up to a higher value...

There may be other side effects that make sense, but looking over the other pacts, but looking at them and talking out what they are supposed to represent, most of them really are already well represented by the effect they offer, even if the balance may be a bit off.  You could do something funky, like for the culture pact, have the other race's culture bonus apply to your ships as well in both culture zones... but again with the increased coding difficulty and probably the need to consider it a higher-end pact.