I have the opposite problem. Spam filtering was working great before the update but after upgrading to Sierra many of my non-spam messages are winding up in Junk. Even after I mark them as non-junk, similar messages (e.g. newsletters, order confirmations) wind up in the Junk folder. The end result is that I see all the spam messages anyway as I scan for false-positives.
It's bad enough that I'm willing to start over with the spam-filtering algorithm and spend the next month "training" it to recognize spam. Nuking its database (after backing it up, of course) may be the only way out -- if I can find how to reset it. This might make things worse, but spam filtering is so horribly broken for me that it's worth a shot.