We saw them build two Delta Fliers.
If they can't build "torpedoes" when they can build Super Shuttles with a full and new compliment of torpedoes, well then that's just ridiculous.
They had to spend a week upgrading their workshop.
It's not a big deal.
In the Omega Directive we saw Tuvok build a super bomb.
Whatever they couldn't do in the third episode, they got over it.
Although I would have liked to have seen them borrow from the species they met if the bad guys were using better weapons than Photon Torpedoes then who ever was down int he workshop should have been able to reverse engineer what had almost kicked their ass... And if there was a work shop that could make anything, then there's no reason that once they got in touch with earth that they could have and shoud have been building quantum torpedoes if even Quark could sell them to the 20th century Military.