” If someone is not Shomer Shabbos, they won’t be counted for a minyan”
The universal custom is to count Jewish men above bar mitzvah age for a minyan as long as there isn’t some other disqualification (such as having converted out or married a non-Jew). But being non-shomer Shabat is not one of the disqualifications. I have seen this done in many charedi shuls as well as MO shuls.