With the current state of affairs, I don't think the arbitrary system of health is needed.
Shredders, as pointed out, do not farm anymore because of the expodential costs for caps. Farming is still possible, but its farming in general, not being tied the hp directly.
For the vampires, I think high health has the opposite. When the vampire attacks a small health unit, it kills it quickly, reducing fleet battle dps more rapidly and allowing the masses of vampires to concentrate attacks on a smaller group. There is no real lag time in team fights because all the targets are bunched anyway. When it whacks larger targets it takes longer for the vampires to concentrate fire and attack (if not microed). The only theory I can see to why you'd ban the vampires is because you'd have them be able to attack the same target 30x before it dies as opposed to 10x, but as I pointed out earlier in large fleet battles it doesn't take more then half a second before its attacking at full speed again.
In conculsion, I feel like the limit nerfs shredders and vampires a little on normal and above, and really hard for us who use low caps or worst. If the limit was determined to still be needed, it should be on the ships themselves and not on their given health. So starships and buildings and super low cap fleetships could be banned, but others are left alone.
Agreed, keep the split, but hand out fusion cutter immunity to only things that need it, instead of automatically handing it out based on health.
Things that should probably keep fusion cutter immunity are ships with the "all attackers get a Nx bonus against me" (this mechanic wrecks havoc with "effect based on damage amount I inflicted" mechanics. Z mirrors + viral shredders lead to some pretty amusing oddities before Z mirrors were given fusion cutter immunity), things that are already supposed to be immune to melee attacks, and command stations that currently have this immunity (military, human home, and AI home command stations)