I come across this on almost all designs I do. And the answer is always the same.
Place all the pins on top of each other in the schematic symbol, such that their 'active' ends coincide. Hide their pin identifier and name. Place free text in the schematic indicating the internally connected pins, their pin numbers as a list and and their function. E.g.
I'll update my answer with some pictures as an example next time I'm at my CAD PC.
In the PCB just reference all the pins by their ID and location normally.
That way in the schematic a single connection to a pin completes all the connections in the PCB. The schematic becomes far less cluttered. It becomes impossible to accidently connect pins wrongly.
The only danger with this method is that it hides the 'single pin net' DRC error. Because of this it's important to make sure it's obvious the pin should be connected to a valid signal or power source within the schematic symbol drawing.