The problem with that theory though, is that they couldn't marry without his permission - and he could easily throw the ambitious noble in the Tower for marrying them without his permission. I'm not sure that would make them very attractive as a bride.
Yes, Richard III had reason to want the boys out of the way, but he easily could have arranged for it to appear as a natural illness-related death for one, and then a week or so later for the other. A huge state funeral, Richard appearing the grieving uncle, and while some may have been suspicious, it remained a fact back then that people died of illness all the time.
I suppose another option could be someone arranging to murder the boys, Richard's men finding the bodies and Richard opting to hide the bodies rather than allow suspicion to fall on him. But I don't think that could be contained as a secret tbh.
It's more likely that someone else (ie Margaret B or Buckingham) had hired a couple of their men to gain access and spirit the boys away - either gaining their cooperation telling them they were helping them escape and then murdering them elsewhere or murdering them in their room and carrying out the bodies. It's possible, I suppose, that the boys were drugged if someone had access to their food, so it could be accomplished easier as well. It makes the most sense, and as secret as it is, that generally means very very few people knew about it - no surprises, as that's generally talked about.
For them, the bodies being gone meant that a- nobody could do any investigations that might prove them to be involved and b- it made things very uncomfortable for Richard as he couldn't them defend himself by showing the boys or blame anyone else by showing the bodies. Yes, there is a possibility that Richard was behind it, but he'd have to be pretty stupid to do it in that way, as suspicion was very likely to fall on him, and change his morals very quickly as he'd always been loyal to his brother no matter what.