Well, yes, but with a disclaimer. Tour operators will not take you to areas if the current or waves are too strong, opting for other, calmer waters. That said, the currents around the Nusa Islands are a little unpredictable and if you are doing a self-guided snorkeling trip you should be aware of the risks and take precautions.
If you are starting to tire, turn back, particularly if you are at more difficult spots like Manta Point.