It's a shame there isn't an option to decommission ships at shipyards or something to recover some of the resources. I always feel bad blowing them up since you never see the crew leaving...

That sounds like an interesting compromise, what other suggestions do you have for something like this?

Another option is just a plain refund at scuttling, which was present in Sins 1. Maybe then a plus modifier with a repair bay/component shop/(frigate) factory present. That would be in the same style as current component (item) building.

I'd have an ability on shipyards (maybe unlockable?) which would disable/pause ship building while it deconstructs a selected ship, that way you have to balance building vs deconstruction. Not sure if you'd want to micro it on every ship - I wonder if there would be a way to multi-select ships in range, or order them to queue up for deconstruction... This would encourage having more worlds with shipyards to deconstruct ships, as in my playthoughts I don't build many shipyards at all.

Have the refunded resources be a % of the ship's initial value, which is further reduced by the % of the ship's health (so it can't be exploited as a way of getting around repairing ships by deconstruct > build new ones).

if you blow up all research stations you lose access to any completed research, eg new ships etc. Unless that changed in the last patch or 2.

This is just false. As long as you researched the Tier, you're good.

I do think the research is slower if you delete stations, but I'm not entirely sure.