As covered by The Verge, the developers for the emulators had received communication from Discord about how they were supposedly sharing content that violates intellectual property. In a statement provided to The Verge, Discord said that there was a court ordered injunction for the takedown of such materials, suggesting that the action is directly linked to the previous legal issues surrounding the Switch emulator Yuzu.
"Discord responds to and complies with all legal and valid Digital Millennium Copyright Act (DMCA) requests. In this instance, there was also a court ordered injunction for the takedown of these materials, and we took action in a manner consistent with the court order."
What's unclear about this development, however, is that it's not obvious as to whether the Discord channels themselves were actually violating IP rights. The developers had previously stated that they were taking appropriate measures to avoid action from Nintendo, but it is also possible that individuals within the channels were sharing material that could breach Discord's policy.
Even if this is the case, however, Discord's Copyright and IP Policy states that only specific content deemed to be infringing on copyright law would be removed, while repeat offenders' accounts would be disabled entirely. According to Sudachi's developer Jarrod Norwell, Discord's removal of his account came out of the blue with very little supporting information to justify the action.
As such, it seems that the removal of entire channels and developer accounts is a case of 'dotting the i's and crossing the t's' for Discord, and it's likely that the company would simply rather avoid the wrath of Nintendo entirely. Hopefully more information will come to light regarding the issue, but it certainly seems like Nintendo is on the warpath regarding Switch emulators.