phish, a points assessment has NOTHING to do with visa refusals. if you had applied for and been denied an E.C., then yes. but merely not meeting the criteria is totally unrelated. i mean, does every PBS wannabe get the points? no. so are they then to consider themselves visa rejectees for the rest of their lives? certainly not. frankly i think you might be being a bit paranoid about this!
plus i know someone who was (mistakenly) rejected for Hsmp points (at the letter stage); she's a frequent traveller and (rightly) never mentions this on forms. gets visas from all over, no problem.