When it comes to point cost I honestly don't see an issue. When discussing space issues its going to boil down to how "accessible" those weapons are. If I have a thousand seekers on board my ship and I can only launch them one at a time there use is extremely limited. If however I can launch them all at once as independent self guided spacecraft there usefulness and value increases exponentially. 

As I said before I found it very interesting that this is exactly what ends up happening in the "Honor Harrington" universe. Ships become little more than hollow missile packs due to technology allowing ships to depart from using "traditional" launchers. Naval warfare simply shifts to who can launch the most missiles, from the greatest distance, first. ...in my personal opinion kind of boring.

Seeing as I started this mess I should at the very least offer some solutions.

1. Make non-launcher seekers externally mounted. They are literally attached to the hull and so may be launched in any number desired. However you can then only mount say twice or three times the hull value to limit the number of seekers carried in this way. So a hull 10 ship could carry and launch 20 or 30 external seeking weapons. Remember the space of a ship takes into count its internal volume, if seekers have an unlimited launch rate we must assume they are open to space otherwise they would need a mechanism to move them from internal storage to a launching point, a.k.a they need a launcher. There is only so much surface area on a ship.

2. Require seeking weapons to be under the launching ships control. Modern weapons for all their guidance capability are still for the most part under human control even when they are moving to their target. There remain serious moral implications for removing the human component from the attack equation. So an easy solution is to simply set a launch limit on the number of seekers that may be controlled at one time by a single ship. This keeps players from simply turning there ships into giant missile packs for a single launch strike.

Additional options here could be for ships to hand off responsibility for controlling seekers to other friendly ships in their battle-group. Or even mounting special equipment to increase seeker control limits. Could also be interesting if you could kill the controlling ship and your opponent would then lose his launched seekers, something like what used to happen in Vietman when Intruders flew "Iron Hand" and allowed themselves to be missile targets to kill the launching radar system. This would discourage people from building hollow shells to quickly launch seekers.

3. Require seekers to be launched from a magazine, and the number of mounted launchers then controls the seeker limit.

Or do all three.