I remember seeing advice in the past to never research the minimum engine power techs because your shipping lines would use them and become less effective.
Does this still hold true?
Mixed results. It's true that the civilian ships will be slower since they use the highest level of this tech, but they will also be cheaper to build since engines are a major cost and especially are the dominant cost for freighters - cheaper ships also means more ships, which can roughly balance this out. A size-50 NGC drive with 50% efficiency (250 EP) will cost 62.5 BP per engine, while the same drive with 25% efficiency (125 EP) will cost a mere 15.625 BP per engine.
There are two factors to think about: one is the law of diminishing returns, at some point the engines will be so cheap that the benefit of making them even cheaper is minimal, especially for the more costly colony ships and fuel harvesters. The other is game performance, as more civilian ships means more calculations and thus slower increments. The recent change to make civilians build only their larger ship classes after certain breakpoints helps with this so it is a +/- thing, but still a consideration.
One suggestion for how to handle this is to manually un-research the tech levels you don't want the civilians to use, and manually re-research them when you want to design an engine with that tech (which should be relatively infrequent, once or twice per engine tech level as you only need one big commercial engine for most purposes). If you are worried about it you can do this, however in practice I usually only worry about the first 1-3 levels of the tech so it doesn't concern me enough to bother.