Eagle - placing pin number silkscreen
The industry standard is to place a pin one indicator when you make the PCB footprint or to make pin 1 square and the others round. Anything beyond that you add manually to the PCB. 

I personally don't annotate the schematic.
However I find adding the actual signal names to the bottom silkscreen a lot more informative than the pins numbers:

(Company name has been removed)
You can also see that pin 1 has a square solder mask, the others have a round solder mask. 

If you work in a company with a PCB lay-out team you normally have to give a lot of instructions when you hand over the design. Those can contain anything from detailed component placement to what should be on the bottom and top silkscreen.