I'd think that because they were of the circular "standard" airlock variety the intent was they were supposed to be accessable to travel pods, etc. - refit Enterprise had other docking ports and EVA hatches that weren't the standard variety, it seems if not intended to made with the standard collar, a rectangular shape would have been a better choice for that alcove (I'm not sure we ever saw the starboard hatch cover open, only the port, so I guess the starboard side could be a different type of hatch).
Circular apertures are structurally safer and more efficient than rectangular apertures because corners in rectangular door openings act as stress multipliers when the bulkhead the aperture is located in is subjected to stress. This is particularly true when there is pressure difference on either side of the closed aperture.
So I think it is reasonable for any external hatches on a pressurized space ship to be circular unless there is compelling reason requiring the hatch to be a different shape.
As to docking with the recessed circular hatches hidden behind panels on the undersides of the refit enterprise saucer, then problems are:
1. It is damn inconvenient to have to fit into the recessed alcove to dock. If those hatches were meant for convenient access by docking shuttles, they can be located directly on outer hull surface instead of being recessed in alcoves behind panels.
2. The travel pod docking port has a ring of docking hooks which pivots out to grasp the inside of the circular rims of enterprise's docking ports. The hooks are visible in TMP and their functions explained in a number of authorized blue prints. This means the docking mechanism is not ambidextrous. Instead the shuttle side forms the male part of the docking mechanism, and starship docking port forms female side. The male docking hatch has to fit into the recess of the female docking hatch for it to work, and female docking hatch on the star ship side must have deeply recessed doors for the male side on the shuttle to engage. The doors behind the panels on the underside of the saucer were not deeply recessed. So travel pod and shuttle docking collars won't engage.