That's a valid and important distinction, but it still seems that anything that can't be examined is mere speculation rather than actual science. Otherwise anything from Flying Spaghetti Monsters to magic becomes a sound scientific hypothesis if it doesn't conflict with known facts and one simply dismisses the absence of confirming evidence as human and/or mechanical inadequacy. Pseudoscience subsists entirely by applying that logic to anecdotal evidence that defies controlled experiments, but I doubt your intent is to put dark matter in the same class as ESP and astral projection.

It's not a problem, as such, but it means simply eliminating all hypothesized examples of a given theory isn't enough to refute it, and that eliminating all hypothesized alternatives isn't enough to vindicate it. To use a convenient example, invalidating all known MACHO and modified gravity theories gives exotic dark matter no additional weight; there could still be a valid but undiscovered normal dark matter or modified gravity theory. Ultimately it's a good thing because it requires any theory to stand on its own rigorous merits, but it also complicates things because you can't establish the improbable as the truth simply be eliminating everything impossible.

It's a Boolean equation; either baryons are conserved or they aren't. However uncommon or unlikely their natural decay, if it occurs it occurs, and violating conservation of baryon number ceases to be an obstacle to MACHOs as well as to the various Pati-Salam alternative GUTs. It disqualifies both or neither.

It's also wrecks credibility with perceptions of The Scientist Who Cried, "Wolf". Slow and steady wins the race, to conflate fables.