I want to make a 5/8" opening in the super to reduce bee travel distance and increase honey production.
Will this actually help with honey production and will the bees find its way to the hive when I remove the supper?
I use an upper and a lower entrance on all colonies, all the time. If they aren't guarding any entrance properly I will reduce it to very small (lower entrance) or close it entirely (upper entrances.) I let the bees decide which entrance to use, for which purpose. Most of the heaviest foraging appears to enter on the top, at least early on in the season such as now.
I don't put extra holes in my boxes, though, I use a 2" shim above the highest box in the stack for the upper entrance. The "standard" upper entrance is a 1" diameter hole. I will add additional holes if the bees are highly upper-entrance oriented, or reduce it to a smaller one if they aren't. The 2" high shim can result in comb built in the void, or hanging down from the underside of the inner cover (less so on the hives with fabric-floored quilt boxes on all the time.) A lower shim such as an Imrie shim might be a better choice if that would bother you. Keeping the bees generously-supered reduces the amount of comb inside the shim.
A single, full-width entrance below the boxes is an artifact of Langstroth hive design. It may not be the way the bees would make it, if they were choosing things.
The one significant drawback to a primary upper entrance vs a primary bottom entrance is that you are disturbing more foraging bees whenever you have the stack open for inspections. Because the expected entry point has been removed. I moderate this somewhat by taking but the lowest one off and restacking them in reverse order on a temporary base just in front of the hive. I top this stack with the upper entrance shim (and a lightweigt lid) so an entrance is near-enough to where it is expected that foragers enter the stack fairly normally. I inspect the lowest box, then move the next lowest one back for inspection, etc., always setting the upper entrance shim down on the highest box in the temp stack.
I dont want my bees using an upper entrance, and I certainly dont want entrances in my supers. We use bee escapes to pull honey, and an entrance above the escape is just an invitation to rob the supers empty after the escapes are on.
I run a cloak board on my starter/finisher used for raising queens, so that colony has an upper entrance by design. The top box in that colony has 3 frames of pollen, which I consider a great thing in the queen builder as it puts pollen frames right beside the grafts when they go in. But this makes me wonder how many frames of pollen I'd end up with in the honey supers if we ran an upper entrance... I'd rather have pollen frames in the brood nest for the most part, not in the honey supers.