Skimmer missions were nerfed simply because of the off chance that you could get a really high paying one to a base with literally no security, not even a turret, just an endless stream of skimmers spawning.
The nerf to these took 2 forms. 1) Skimmers would no longer continue to spawn after each wave was destroyed UNLESS you were in the SRV. Fair enough in a way, why would a base continue printing resources that could not function as intended (skimmers can't reasonably attack ships, only SRVs), and 2, the payments were reduced (not dramatically, but enough) across the board, to reduce the amount of reward that could be gained, so that they didn't have to balance the payment based on the security of the base (in other words, so that if you get sent to a low security base, you can't get paid too much, ,with the result that the payment is not even remotely worth it if you go to a high sec base (the majority).
It has always been the case (as it should be), that skimmer kills satisfy 1 kill per mission, PER FACTION. So, if you have 2 missions for 6 skimmers from the same faction, you need to kill 12 at the target locatoin. If you have 6 from one faction and 6 from another, they will complete at the same time.