A comprehensive general rule is impossible
Of the game's two thousand or so feats, there are about 40 feats like the one the question describes. That is, the feats have sneak attack as a prerequisite, and they require the attacker to spend sneak attack dice to realize a different benefit. About half of those feats—so about 20 or so—are like the untyped feat Deep Poisoning (Dragon #322 37): outlier feats with no connection to other feats, their individual mechanics dictating the rules for their use.
This means the feat Deep Poisoning stands alone and can only be examined in isolation. It begins its benefit by saying, "When making a sneak attack with a poisoned weapon,…." To this reader, that indicates that if the attacker can't deal sneak attack damage to the defender, the attacker can't realize the feat's benefit. Against a shambling mound or vampire, for example, the typical attacker just won't be dealing sneak attack damage, so unless the attacker has a way to make sneak attacks against such creatures, the attacker can, essentially, stop trying to make the feat's benefit happen after word number five.
Whether other feats work in a fashion similar to the feat Deep Poisoning will depend on the feat.
However, there are rules for ambush feats
The remaining 20 feats that allow an attacker to cause a different effect by sacrificing sneak attack damage dice are classified as ambush feats. The final description of ambush feats, in part, says
Ambush feats… allow you to use your sneak attack ability to deal an additional harmful or hindering effect upon an opponent, at the cost of one or more of the extra damage dice you normally deal with a successful hit. (Drow of the Underdark 53)
In other words, for the benefit of an ambush feat to be realized, the attacker must already be able to deal sneak attack damage—and, in fact, must still deal at least +1d6 sneak attack damage to realize the ambush feat's benefit! These feats are clear in how they work, and they all work the same way.