does this affect the campaign at progress ? do you get any alternate mission / ending with it ??

its been 15 years since i beat this i forgot almost everything lol i remember not doing all of the extra objectives that's why im wondering do you get anything if you completed all of them ? [</span>

IIRC there might be a few instances but it's mostly that a capital ship destroyed in a mission won't pop up later in another, the campaing overall is linear Tie Fighter-style.
Only Freespace 2 has an alternate ending if you fail to get away in the last mission.

Sometimes things carry over to later missions and you can also get alternate missions. E.g. when you save the Malta (Aeolous) in the second-to-last mission, it will appear in the last mission and help cover the evacuation. And the number of turrets and flak you destroyed on the Sathanas also carries over.

Also, if you fail any of the "Secret Service" / special operations missions or don't get all their objectives (while surviving and not getting executed), you can't do the following secret service missions and get thrown back to the main campaign.

You also get two optional fighters (a fighter and a bomber) in Freespace 2 if you finish the optional missions. It's the Ares and the Artemis D.H.

And as has already been mentioned, there are 2 different endings to the campaign.