Any CEs that are just not worth keep at all?

It’s best to keep all 4 star CE, burning them would just be a waste.

And for 3 stars CE keep event exclusive ones, and use the others as CE bombs to level your higher CE.

You can keep some of these SR CEs due to re-run events. And also 3 star event CE.
Some specific low-tier CE are still useful since your team Cost is always limited (Even in JP serve). Some 3 star CEs still worked if you MLB it, or even not MLB it.

Like you mentioned
Necromancy is a RNG gamble. I have see 7 times guts for one servants with that.
Gentle Affection is not bad of MLB to Medea Lily, Iris. Only their bond CE could exceed that. And there will be re-run event need that CE.
Original Legion is not bad to be equipped to servant relied on strong ST NP, like Cu.

Quite a few bad CEs actually, including the event one maid in Halloween. Unless you can MLB it, I'd just burn 2 copies and keep the third.

I've got more suggestions, but of course how bad they are depends on whether or not you have/use servants that can effectively make use of them.
- Record holder: +25% debuff success rate. Not particularly useful.
- Art of the poisonous snake: +30% arts increase for 3 turns. Not a bad buff, but only lasts for 3 turns, so after that you'd effectively have nothing. Only worth it if the quest only lasts a few turns, in which case, it's so easy you don't need it anyway.
- Code cast: +25% ATK and DEF, again for only 3 turns.
- Golden millenium tree/Ideal holy king: Increase max HP. This opinion will probably be a bit controversial, but there are much better ways to boost your team's durability than a max HP increase of 2000 - 3000 HP.
- Any < 3 star CE that isn't MLB dragon's meridian. The rest come often enough that imo it's worth MLBing at least one of each, but most aren't worth keeping more than 1 copy of.

These are all just CEs that I have, there are definitely more I just can't remember them all.

Having said, that, personally I would still advise against burning 4 star CEs unless you desperately need the resources. You never know when you might change your mind about them, and it's possible that you may never get some of them again.

Necromancy sounds good if you have rank ex+++++++ luck. Pretty much useless otherwise. My main problem with it is that you CANNOT use guts along with it even if it necromancy effect doesn't proc.

If a CE seems a bit niche then i'd recommend getting one MLB copy and then just burn the others from there but I usually like to have 3 of the more useful ones like starting NP (DM, IE, Kaleidoscope) and such. Almost all the 3 star CE's can be burned though if you really want to none of them are breathtakingly amazing or anything but I would again recommend keeping one MLBed version of each in case you need to save cost in a team comp.