Short answer: Yes, they can see it. Thermal information is processed in the visual center of their brain.
This means they also see the heat from their heat tape, UTHs, and the red bulbs they supposedly can't see. (Although, IIRC, pythons can visually see the color red.) That said, it's likely the other end of the spectrum that their internal systems interpret as "daylight," and is thus disruptive. In thermal, the world is still crazy bright after dark, but it's a different source of light. They can certainly tell the difference.
Ball pythons have dichromatic vision, and there is even a possibility that they are trichromatic. But regardless of whether they can perceive the colour red, they can certainly see the light itself. If it's being used overnight it's best to use a heat source that doesn't emit light, like a CHE, to avoid disrupting the snake's day/night cycle.