Does drilling a hole in thermostat affect engine temperature during cruising speed? (Please read my explanations before answering)

Yes, you can drill a small hole in your thermostat if you're bothered that you won't be able to bleed the system without it and no, it won't make any appreciable difference to the operation of the system

If you think about it, the effect of turning your car heater on will have a greater cooling effect on the engine than allowing a 1 mm wide low velocity stream of water through the radiator. If a car engine could be effectively cooled by a tiny stream of water then radiator hoses wouldn't need to be 2-3 inches wide

If you remain bothered about drilling a hole perhaps instead consider wedging the thermostat open a tiny amount using a chunk of something that will melt (wax) or dissolve (a fragment of a boiled sweet)* so that it will go away but honestly, as the commenters have indicated, the designers of your car's cooling system knew what they were doing and unless you're certain that your car came with a holed thermostat (that you've since replaced with a non-holed one) and you've certainly caused yourself a problem, then I wouldn't worry about it

* _{I wouldn't personally do these things because I don't think there is a need, but i offer them as ideas because it may help you sleep at night}

Waste of time. Air can already leak through the thermostat.

Thermostats are baffles, not seals. The difference is a seal prevents all flow, a baffle only prevents significant flow. Baffles are used when the same fluid is on both sides and when a small amount of leakage is tolerable.