ST Protect rarely seen in PuG

2. Inverse synergy with MMs, to the point where ST rits are completely useless in most areas with MMs. MMs are extremely powerful PvE builds and they also do damage which makes them much more popular by #1. Probably 3/4ths of PvE groups are using minions of some kind so that throws out ST rits for all but 25% of groups. This is a common misconception. Minions minimally increase the drain on the spirits. Let's compare the scenario of defensive spirits with no minions (SitA) with the scenario of defensive spirits with minions (SitB) and work through this step by step.

Displacement:
In SitA monster X attacks a player. With 75% likelihood, Displacement triggers and loses hp. The full damage from the attack is prevented.
In SitB monster X probably attacks a minion. With 75% likelihood, Displacement triggers and loses hp. The full damage from the attack is prevented.
So, what's different? Almost nothing. The monsters generally do not get to make extra attacks because minions are present. It's just the same attacks getting blocked either way, only the targets are different.
The only potential difference is AoE. Dervishes and Barrage users and such may score extra hits by virtue of there being more targets.

Union:
The analysis is identical to the analysis for Displacement.

Shelter:
In SitA monster X attacks a player. The damage is reduced by the player's armor, then checked against 10% of their max hp. If it's over, Shelter triggers and loses life. The damage beyond 10% of max hp is prevented.
In SitB monster X probably attacks a minion. The damage is reduced by the minions's armor, then checked against 10% of their max hp. If it's over, Shelter triggers and loses life. The damage beyond 10% of max hp is prevented.
So, what's different here? Three things, potentially.
First, there's the same AoE issue. AoE might cause Shelter to trigger more simply because there's more things to hit.
Second, minions have different armor than players. At 16Death+Masochism, horrors have 80AL, fiends have 60AL, and bone minions have 42AL.
Third minions generally have less health than players because they don't get runes and weapon mods. And bone minions have significantly less life because of their lower level.
The combined effect of #2 and #3 is that a hit which would do <10% damage to a player might maybe do >10% damage to a minion. Most of the time, a hit is going to be over for both or under for both, but a few hits near the border will go over on minions but not players.

Generally speaking, horrors will be more likely to take a >10% hit than a warrior, but less likely than most anything else; fiends will be marginally more likely to take a >10% hit than casters; and bone minions will take a >10% hit a lot more often than players. That's a pretty decent reason not to run Shelter together with bone minions, but not much of an argument against the others.
(There's also the possibility that SY! will make all the players much less likely to take a >10% hit than any minion, but, as you say, Shelter is wasted in that situation; so you might as well use it to help the minions.)

So, in sum, your spirits are generally only going to drain out a little faster using minions than not using minions. (Except bone minions, which will drain Shelter very quickly.)

The other concern about running Shelter and minions is the possibility that Shelter is your only wtfpwn preventer. In that case, even a tiny bit of downtime on Shelter can be really costly. It's debatable whether your team build flaw is that you brought minions or that you didn't bring PS.

Use ST with a spirit spammer instead MB. Or use a MM without death nova and bone minion(like AotL+Bone Horror), who focus on create long lasting minion. End of the problem. It is not so simple. There could be several reasons why you would want to bring a minion bomber. If there are no human MMs and you have to bring a hero MM, you probably want the hero to play a minion bomber because that is the role that heroes excel in. Besides, a good minion bomber bar provides excellent damage and decent tanking even in HM for most areas.

In other words, human necros are better at playing the role of a regular MM where you rely on damage from your minion attacks and you preserve your minions as much as possible for tanking. Not many human necros like to play this role though, because it is a tedious role. On the other hand, hero necros are better at playing the role of a minion bomber and of course they do that well and willingly.