But yeah, I can see Heath getting a supporting actor nod!
Joker is such a showier part than Batman that it's relatively easy to "steal the film" in such a role. (Not to take anything away from Christian Bale, who is also a great actor.) The same was said for Nicholson and Pfeiffer in their villian parts — that they stole the picture from Michael Keaton, who (no fault of his own) was stuck in the straight-man good-guy role.
And it's also pretty common for the Academy to reward passed-over actors with an award for the next thing they do. Denzel Washington comes to mind...