Some opinions from observations. Caution: some may disagree:
The "vent" hole on the early top-mounted wiper motors was intended to be at the bottom of the installed motor-- as evidenced by brand-new unopened motors and looking at the stamped TNK or ASMO lettering facing outward as you would read them. Since years have passed and covers get removed and replaced, some of them very well may be repositioned with the "vent" opening at the top of the motor.
The "vent" would likely operate as a drain for any moisture condensation accumulation within the electric motor section of the unit, and allow for any venting of the motor.
Similarly on the later single motors mounted outside the truck at the base of the windshield, the cover gasket is three-sided and has no bottom section, and the bottom lip of the cover stands proud of the windshield gasket-- allowing for drainage, again from any moisture that may occur inside the cover. It also allows for any venting that could be for the motor. But that doesn't answer the question of the hole smack-dab in the center of the cover, the rubber plugs that sometimes are there, or the covers with no hole in them. The various motors all seem to operate correctly with or without the hole. And, it cannot be for the ground screw that appeared on the inside of the later covers.
So, agreeing with the initial question: why the heck is there a hole drilled into some of the covers? Was it a later correction made by the engineers to deal with an operating issue? If so, why wasn't there a "recall" to dealers to either retrofit the new-style cover or simply drill the hole? Why is the hole in that location, and why do some trucks have a rubber plug there that proves nothing?
Perhaps someone on here who really knows small electric motors can offer an explanation.
Or................was there some devious person on the assembly line with a drill that took out his frustration on random vehicles as they rolled down the line past his/her station?
(Editor's note: please take notice of the previously politically correct "his/her" used above, which arguably might need changed to "her/his/its/theirs/undecided". Apologies in advance for any up-to-the-moment incorrectness. And, should this thread be visited sometime in the future, say the year 2050, please do not blame my offspring for my lack of knowledge of the latest/greatest way of referring to ourselves (or did you change it back to ourselfs), (or as Thomas Jefferson might have written, "hif" or "herf" since they still had not learned how to properly write the letter "s" way back then, and apparently all suffered from the same lisp, or "lifp".))