There’s an interesting breakdown of the uses of the transport ships in this video:
https://www.youtube.com/watch?v=wzHK10-sRzA&t=303s
Basically, he comes to the conclusion that they were just thrown into battles to draw fire from the more important ships.
I’ve heard an interesting bit of lorecraft where the ships were used to bolster the shields of the capital ships with their own shields, which makes a bit more sense. Basically they could act as external shield generators.