Yes, they recognise them. It is not so hard. A teacher in a large school might have several hundred students, and know each one by face and name and target grade. A CEO of a medium sized company might pride themselves on knowing by name all of their several hundred employees.
The Speaker of the House knows by name and state all 435 members. It's harder to recognise someone in a mask but not impossible. And although the Representative do not have assigned seats, however Democrats tend to sit on the right of the centre aisle (as viewed from the presiding officer's chair) while Republicans sit on the left.
One of the purposes of not having the speaker herself preside over most debates, but allowing a junior representative to take this role is to allow new House members to learn everyone's name and face.