OK, I did a test of this. I switched a fighter squadron into Pe-3, set them on day missions, waited a turn, and launched an airfield strike at that base. The Pe-3's did not come up to fight in their own defense. I did a bunch of ground strike missions in the vicinity, no response from that squadron. Ended the turn, now playing as the Soviets, launched a bunch of ground strike and airfield attack missions from that base and the Pe-3 never activated.
Loaded up another game as the Axis and set a night fighter squadron to day missions (flying Ju88 C-6's), and they did activate in defense of their airfield, and also flew interception against a Soviet ground attack on a nearby hex. But when I switched over to the Axis and tried to launch attack missions from that base, they never activated.
I can only conclude that there is some either bug or undocumented feature that prevents air units equipped with planes historically used as night fighters from being assigned to escort day attack missions.