Yeah, from the looks of things, Shinjoebi did switch from Roy as in September which is when the latest PR was posted in the PR thread:
http://smashboards.com/threads/smash-4-power-rankings-directory-project.401710/, and Shinjoebi was listed as Roy. Now and from what the commentators said in his set against Ganon the Beast if I recall correctly, he switched. I don't know when, but he switched. Looking up "shinjoebi (greninja)" on Youtube had October as the most recent time he's used Greninja. 9th in October's monthly:
http://umnsmash.challonge.com/OctMonthS4Top32, and 3rd in November's:
http://umnsmash.challonge.com/NovMonthS4Top32 and in October's Smash in STC 10/24/15:
http://challonge.com/STCOct15Singles. Also got 5th in Sm4sh LL #10:
http://sm4shll.challonge.com/LL10Singles. With Roy, 9th in Go4 Smash Weekly: Sm4sh 9/19/2015:
http://umnsmash.challonge.com/go4weekly1, 7th in LL #8, #7, 13th in LL #6, 5th in LL #5, 4th in LL #4.
He seems to place similarly with Greninja, albeit it's rising rather than falling like with Roy. I don't know where his tag comes from, but he really is a shinobi if he continues to play Greninja. So, just a good player who happens to use Greninja and who happened to use Roy?