SNES VC is n3DS exclusive, so we need to support emulating it's features for it to work. In this case it's using the extra CPU.
New 3DS mode is already supported. It should be fixed by now @Schplee Could you test and let us know the status of this issue?
Confirmed that New 3DS support resolves this issue. Solved by #5117 and B3n30's PRs
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SNES VC is n3DS exclusive, so we need to support emulating it's features for it to work. In this case it's using the extra CPU.