Yes, there's no option to drain all, deducting the necessary fee.
What I did in the past was withdrawing funds in many batches.
In your case, withdraw 90k, then with the rest withdraw again, leaving the 1% of fee of remaining balance. And repeat the process until you remain with 1 sat.
If you're self hosting your lndhub server, you can modify the source slightly to allow zero fee transactions. The error you're getting is the server reserving a minimum percentage for fees and it's set at a minimum of one sat. If you're using lndhub.io public wallet, you can empty it in chunks. Unfortunately that last sat is stuck there IIRC