How do you make point defense prioritize targeting seekers?

The problem may simply be in the timing. The PD fires at the enemy ship, and is reloading when the missile comes in.
If you put the targeting to the view, are the PD weapons correctly targeting incoming seekers (does the targeting change) or do they keep targeting the ship?

Also, I Assume you let the ships do the shooting on their own, and don't click on the enemy ship to target it.

Once the PD has fired on the enemy ship,it can't change its target to a new one (seeker) until the current target (ship) is destroyed.

Actually, the target can be changed even if target is not destroyed, it depends on what the targeting parameters are, but for example using nearest(absolute) shows this very well.

Seeing the long reload times, I think what happens is this:
PD fires at the ship.
PD is loading, while the missile is fired. PD changes targeting to the missile
Missile approaches, and hits target, because PD was not able to fire (it was reloading all the time the missile was in range)
PD changes targeting back to ship, as there is no more seekers.
repeat.

Try the following: make the PD do only one or two points of damage, but make it shoot every 300 ms. See if it still only shoots the enemy ship, or if it now fires incoming missile.

I think the main problem is that you are trying to make a weapon that is both PD and anti-ship.

As is, it sounds like SE V is probably not even programmed to handle such a 'dual purpose' weapon with any effectiveness, at least not without overhauling the strategy used by the ships carrying the weapons.

My personal opinions of this idea overall idea.
Generally speaking, any weapon capable of shooting down things like missiles and fighters is going to be next to useless against a ship, and anything packing enough punch to take on a ship is generally going to lack the accuracy and tracking speed to target smaller high speed targets.
And if you are trying to make a weapon that is good at more than one thing, it is going to be less effective in one of those roles, or simply lessened in both roles.

To quote an interesting saying I saw once (in Civilization IV, of all places), which basically said "If you chase two rabbits, you will loose them both."

Possible ideas.
Perhaps you could also put other PD weapon targets (fighters, etc), higher on the list than ships, bases, etc, to reduce the chances of the weapons wanting to shoot at ships only. I am unsure if changing the ranges to engage ships at would be of any use.

Other possible ideas for "Target Priority Order.
Possibly remove "Total Targeted Damage" and "Has Undamaged Weapons" if present, to reduce the chances of the ship wanting to pour all its firepower into a single enemy ship and ignoring everything else.
"Fastest" might be a problem is fighters are in play, unless you don't mind the weapons shooting at fighters before shooting at seekers.
"Nearest" might be a good choice, since a seeker is generally going to be closer than the ship that launched it.
"Least Armor" might get it to help prefer 'weaker' targets such as seekers over that of ships.