Drilling holes will definitely mess up the bike by making the pickup of the bike more lean , it damages the cylinder valves and ultimately harms the engine . Drilling holes should be the last option as it'll definitely damage your bike and in the end you may have to pay a hefty amount to get it back to the stock condition. Theres an alternative Get a bendpipe and muffler from a BS4 and and get it done on a bs6. The whole system The bendpipe the muffler and the underbelly . The con being Heating will be an issue as the bendpipe runs sideways and not under . But it does much less damage to the engine than drilling holes On a long run . That's the only economical option The other two options being Drilling holes And upgrading to a Full system exhaust. Before you proceed Confirm the issue with a professional. Be it a KTM professional or a 3rd party tuning professional.