If the excess shaft is fouling something then that has to be fixed (either by cutting off the shaft or removing the something its fouling.)
If the motor is ever going to be reused with a pinion on the other end, enough shaft has to be left that end.
If the motor is going to be stripped an rebuilt there are sometimes practical considerations to what shaft length is convenient (Probably not applicable as you seem to be talking about the sorts of motor that aren't usually stripped an rebuilt.)
There's a slight weight saving by cutting off the unused shaft (how much does that matter?)
If none of those are an issue it cannot matter much if the shaft is left full length or shortened.
If the motor is ever going to be reused with a pinion on the other end, enough shaft has to be left that end.
If the motor is going to be stripped an rebuilt there are sometimes practical considerations to what shaft length is convenient (Probably not applicable as you seem to be talking about the sorts of motor that aren't usually stripped an rebuilt.)
There's a slight weight saving by cutting off the unused shaft (how much does that matter?)
If none of those are an issue it cannot matter much if the shaft is left full length or shortened.