also usually the NMs where u don't want to SC usually a weapon with a massive white dmg upside means more risk of healing, on those usually (non sc) ws dmg is the best bet
(thinker kin worm)
I assume what you mean is stuff that heals when you hit it with any physical attacks during a certain window (like your Thinker Worm examples). And in that case, you're not wrong... but in those situations I don't even particularly like NINJA thanks to all of the inadvertent auto-attack, regardless of weapon. But yeah, Empy AM3 does add some more risk to something like Thinker (I say this as someone who has definitely killed my party in
spectacular fashion with Empy RNG by unleashing a ranged attack just after Pain Sync and getting AM3+Double Shot+Crits on both shots)...
If it's a "don't SC" mechanic (like a Maju or Glazemane), you just don't want to use a WS that skillchains with other WS in the party. Could go Ten>Ten for any NIN weapon, Shun>Shun for non-Heishi, or pick whatever works with your other members in a mixed party. In this case, more white damage is a plus.
Kin (or Rani, etc.) are different altogether, since they absorb physical or magical depending on situation. For something like Kin, SC really isn't an issue if everyone only uses WS right when it casts a spell (since you're all going at once, no SC). Inadvertent auto-attack melee damage is relevant, but honestly not THAT big of a deal if you're using a stronger white damage weapon. You'll heal it sometimes (during TP moves where you don't turn), but you'll also do more white damage during the vast majority of the fight when it isn't absorbing, which kinda evens things out.
I know we are beating this horse pretty good but what about when Zerk is down?
Berserk up/down alone is pretty irrelevant. It's just a matter of whether you are pDIF capped due to target and ALL sources of attack buffs/defense debuffs: GEO/BRD/COR, Dia, JAs like Berserk/Warcry, food, gear, Relic AM, etc.
You wouldn't make Berserk up/down sets, though you might consider swaps for attack capped or uncapped. Hard to predict exactly how close you are to capping to build a single "uncapped" set, but a general sense of whether or not you're hitting cap would inform your choices for a particular situation. For instance, whether to offhand Fudo Masamune or not (one consideration, acc/racc is obviously another), whether you need additional attack buffs or can let the supports do something else with their limited bubbles/songs/rolls, whether Berserk is even worth using (if it isn't helping you, don't use it and get the defense penalty), etc.
But yeah, obviously when you're already attack capped that affects some things weapon-wise. Kikoku AM and base Atk become useless, Empy AM is still fully effective, Shun TP scaling becomes irrelevant, etc.