The whole point of the "trap" archetype is to trick people (both the audience watching the show, and the characters in the show itself) into thinking the character is female when they aren't. If they were to speak with a masculine voice, the illusion would be ruined the moment they opened their mouth, which kind of ruins the point.
Aside from this, it would also be very jarring to hear a masculine voice coming from someone who does not look very masculine. The reverse is also true: it would be extremely jarring to see a muscular male speaking in a high-pitched soprano voice.
Screwball comedies like Pop Team Epic may use ill-fitting voices for intentional comedic effect (see also: Up), but with "traps", the comedy instead comes from people mistaking them for the opposite gender. Giving them a masculine voice would, as I've already noted, ruin that particular gag, and then there's not much point making them a "trap" in the first place.