Theoretically, having the username and counter options do have a point. If someone knew your master password and knew that you were using PasswordMaker, then they would be confronted with several variables that they would need to determine in order to create your passwords for various sites. The username and counter is simply another one of those variables.
As for the relative security of the cracking the password, well... the password algorithms are already virtually impossible to unravel. If someone had your final password, and somehow figured out how to crack the algorithm(say, several years in the future when these algorithms become outdated) then they would first have to determine if someone used a username, counter, prefix, or suffix, and, if they did use one, what it was, and what level l33t, or not... yeah.. lots of stuff.
Removing the username and counter would make it theoretically less secure, but these passwords are top of the line, so the difference would be incredibly marginal. You won't loose much by removing them. Go ahead.
By the way, nice forum logo. ;)