With the basket in, you’d only see one hole. That’s why i thought it was for vacuuming. I actually find it weird if it’s on the side and on top of the basket not under. Coz what i have seen so far it’s always under the basket if it’s for main drain.
I believe the skimmer is Waterco as written on the lid.
My main drain port was as you described, under the basket. But I think yours makes sense. "Back in the day," the primary purpose of a main drain was for cleaning. Before auto vacs and robots, you either had to run a manual vac on a pole, into the skimmer somehow, or push gunk down your pool finish and towards the main drain and let the drain suck it up (or some of both). With your setup, the gunk sucked through the drain would travel to the skimmer and dump into the skimmer basket first, where the larger stuff would get collected. I'm just guessing, but I think that was how yours works(ed).
If your skimmer is a Waterco, then I think I found the instructions for it (posted above). Or at least a similar model. You need the vacuum plate for optimum vac performance. If there is not one laying around somewhere in the pool junk the previous owner left you, they seem to be readily available online. Check out that PDF I posted.
Now if you're sure that water drained from that upper port when you removed its plug, and you even got some vacuuming suction from it, that remains a mystery. A possible explanation (again, kinda just guessing), is that it was plumbed for other than its intended use. It might be plumbed back to the pad, to a valve that allows you to control its suction, and was "repurposed" to be the vacuum port you think it is. If that's the case, you'd find a valve for it near the pump. There would be a 3-way valve, or possibly two two-way valves, with which you could shut off the port under the basket, and engage suction through that upper port.
The other possibility is that it was plumbed to an open-ended pipe somewhere in your yard, and was being used to drain a few inches off the pool when it got too full of rain water. Do you get a lot of rain in your area?
You're going to have to experiment a bit. I gave you one such experiment above. A second experiment would be to use a rag and seal up a garden hose to that upper port as best you can, and then turn on the water to the garden hose. Does it back right up, or seem to go somewhere? If you can continue to pump water into it, then keep that going and explore your property for a gush of water pouring out onto the dirt somewhere.
Post a pic of all the valves and pipes that lead into your pump. If there are any, we'll show you how to figure out which are which and what they're doing. That might solve the mystery. Also, I think you were asked, did you answer: do you actually have any drains in the bottom of your pool?
To be continued!