In general the use of square pins was only used to identify the first pin of an IC or connector etc.
THis was used by an assembler to aid them in the correct insertion of a component, also a service engineer when the board is upside down to identify pin 1.
However, as said it does cause some clearance problems, and with the correct legend idents it is not really needed for assembly.
It's more down to personal/company preference if you wish to use pin 1 as a square.
In the past I have had square pins for pin 1 also selected when making a solder paste screen on boards that have PTH & SMT components on.