In Fortran 77 (and probably older ones), you require six spaces before each line. This makes it incredibly difficult to golf, so should we count those spaces in the byte/character count?
Yes, count them
Every language has its pros and cons, but that doesn't mean that every language should get special treatment. If the person posing a question wants to set up a complicated handicap system then that's their decision, but the default assumption should be that a code-golf program's score is the size that a tool such as
wc would report for the source file, with appropriate adjustments for special flags.