Henry VII couldn't prove they were dead, because they were AWOL by 1485.
That could be a) murdered by RIII b) murdered by someone else c) dead of natural causes with embarrassing timing or d) smuggled abroad. Wild card e) present & correct in the Tower, promptly done in by HVII.
a) & c) are the likeliest.
HVII needed to marry EoY, to shut up the remaining Yorkists. Her being declared illegitimate was awkward, so least said easiest mended - hence all copies of Titulus Regius, which bastardised all of EIV's children by his queen, being quietly burned.
To make a hooha about TR being probably bollocks, legally, to legitimise Elizabeth, would also have legitimised her missing brothers. Which would have made Edward V the lawful monarch all over again...if anyone could find him. Obviously not in HVII's interests.
It seems that HVII didn't know/couldn't prove where the boys were. So he decided it would be easiest not to comment on their fate at all.
Yes, they were almost certainly dead by then. Also, if they hadn't been, he'd have made sure of it, as he did with the rest of their relatives, & was seen as sensible kinging at the time.