In combat of course you would use hull repair but after the battle or if you retreat to a planet with lots of repair platforms you can fill up your fleets shields.
Shields actually regenerate pretty quickly between battles. If you're anticipating another major battle within 2 minutes or so, I certainly would not be blowing repair platform antimatter lightly, and would conserve it only for hull points.
We're having a problem with the Vasari hanger right now on similar grounds. It's not that producing strike craft is a bad investment, it's that phasic traps put that antimatter to much better use. The weaker ability gets ignored because this is a structure with very tight antimatter capabilities. The same thing will happen to the Advent repair platform if you add a secondary ability, and as a rule shield is less valuable than hull for single-target abilities (they're about equal for multi-target abilities).