The popping sound you are experiencing after installing ground loop isolators could be caused by a number of factors, including a faulty connection or a power surge. It is unlikely that this popping sound will damage your subwoofers in the long term, but it is possible that it could cause short-term damage if it is caused by a sudden surge of power.
To troubleshoot the issue, you may want to try disconnecting the ground loop isolators temporarily to see if the popping sound goes away. If it does, then the issue is likely related to the ground loop isolators, and you may need to investigate further to determine the root cause of the problem.
In general, it is important to monitor any unusual sounds coming from your subwoofers and to address them promptly to avoid any potential damage. If you are unsure of how to troubleshoot the issue, it may be a good idea to consult with a professional or an experienced audio technician for assistance.