Oh well, in the end I have used something similiar:
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$catcount = substr(@$navlink['note'], 1); //remove first character or bracket
$catcount = substr($catcount, 0, -1); //remove last character or bracket
if (strlen(@$navlink['note']))
$this->output('<SPAN CLASS="qa-'.$class.'-note">'.$catcount.'</SPAN>');
}
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This removed the brackets.
That code has to be placed just after the else statement in function nav_link in the advanced theme.