I wouldn't even say that use of a header format itself is indicative of wrongdoing, even if Tomohiro hadn't went on to work for Nintendo.
However, if Nintendo had released any NES ROMs with a "DiskDude!" header? Then maybe. AFAIK this never happened though, and the big leak proved that they had a full final (and sometimes post-final or unreleased final) archive with split PRG/CHR, so they didn't need to use DiskDude! ROMs.
Yeah I think it was just the developer working with what he was familiar with. For example, the emulator used for the 3DS NES Virtual Console titles was developed by a different team at iQue. It uses its own bespoke header format called TNES rather than the standard iNES header.
However, if Nintendo had released any NES ROMs with a "DiskDude!" header? Then maybe. AFAIK this never happened though, and the big leak proved that they had a full final (and sometimes post-final or unreleased final) archive with split PRG/CHR, so they didn't need to use DiskDude! ROMs.