I believe it does, but by the time you start getting HLAs, you're almost bound to have 100% Set Traps anyway. Jan, with 17 DEX and his Gnomish Thieving Bonuses, can get 100% in all 7 skills by Thief Level 23. A F/M/T should be roughly Thief Level 15 by the time he first chooses a Trap HLA....nowhere near Level 23, I admit, but then he's likely to be wearing the Mercykiller Ring as well.
Bards, however, don't have the slightest detail to worry about. Crack open any Bard with Shadowkeeper, and you'll see that their Set Traps skill is automatically set to 100%.
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Volothamp's Comeuppance
Everything you ever needed to know about the entire Baldur's Gate series......except spoilers.
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