It seems to me that when the Emperor sends out his minions (Darth Vader and Inquisitors) to root out all the surviving force users, he would have sent them to destroy The Bendu. In Thrawn: Alliances, The Emperor can detect Chiss Skywalkers, so it doesn’t seem to be much of a stretch to see him sensing The Bendu, a much more powerful force—user who isn’t hiding. So why isn’t The Bendu discovered and/or attacked by the Imperials?
Emperor doesn't really hunt all force users. The Empire is quite practical in this regard - active hunt is out for those that actively resist or present a significant potential threat. That mostly meant Jedi - the natural opponents of the Sith, and natural supporters of the Rebels; others were usually left alone.
Bendu is quite content being left alone, and insistent on his neutrality. Even after Kanan goaded him into participating in the Battle of Atollon, he acted so it was clear that he attacked everyone in his territory equally. So it wasn't really that useful to hunt him down - easier to leave him alone and deal with the situation later. So he might be known to the Emperor, just not seen as a threat that needs to be dealt with urgently.
That said - force detection abilities work in mysterious ways, and it isn't all that clear how "force-hiding" works. For example, Emperor doesn't tell Vader what he has to deal with in the Chiss affair - that might be just him being mysterious, or he might be simply unable to identify the cause of the disturbance. Bendu might be hiding his presence from anyone who isn't on his planet, or maybe his skill allows him to use the Force without creating disturbances that Emperor can perceive - for all we know, his power and skill is greater than Palpatin's. So we can't be sure that Empire ever knew of his existence before coming to blows with him - Thrawn certainly didn't expect to encounter Bendu.