Replacing deck joist - board width mismatch
It's hard to know how much of the 1/4" difference you're seeing is going to remain after the wood dries out.  I'd take just a 1/8" notch out of the ends of the joists so they set 1/8" high in the joist hangers now, with confidence they will shrink at least 1/8" as they dry.  If they shrink a lot and make a noticeable low spot, you can shim between the bottom of the hangers and the joists.  (As long as you have access to the joists when the decking is on.)