Great question. This is a complex subject, so apologies if my explanations don't help!
If you update a cue by simply changing values, you have to think about how the fixtures are going to get to those values, and how the fixtures are going to get from those values to the values in the next cue.
However this is where SmartTag is your friend - if you set a fixture to 0 and update a cue, but the fixture was already at 0 in the previous cue, this operation essentially IS an Update > Remove. This is because SmartTag does not include an instruction for a light, if the light is already doing that thing in the previous cue. So if it was @ 0 already, there's no need to tell it to be @ 0 again. Intensity data is therefore removed - tick. SmartTag also strips out attribute data for the fixture if it is @ 0, hence this operation means all data is removed for the fixture in this cue. However, this then becomes a question of tracking. If you did this update as Cue Only, the next cue will now have data added in, to tell the fixtures to be in the same values, as if the previous cue had never been updated. So in this scenario, an UPDATE > SmartTag > Track Forwards would have been required.
If you use UPDATE > Remove, your cue will have absolutely no instructions for the tagged parameters. The parameters can therefore continue doing what they were already doing, OR Move On Dark can grab that fixture in order to prepare it. This therefore could be a good option if the fixtures were on in the previous cue, and you want them to remain on in this cue with no change.
So the choice as to whether to simply update the values stored in a cue, or remove them completely, really needs to be made on a case by case basis, thinking about how this could effect cue transitions.
When programming quickly during plotting or even technical rehearsal, it may make sense to do a "quick and dirty" update, to just change the values rather than remove the values. Then, run through your cues prior to the dress. If there are any weird transitions, or Move On Dark isn't working as expected, you can then go into the troublesome cue, select fixtures > HOME > UPDATE > Track Forwards > Remove > ENTER if necessary to tidy things up.
I hope this makes sense. Let me know if you have any questions.