What to use as a spacer where deck joists overlap?
Indeed, sistered boards may provide an area that is vulerable to moisture buildup and decay. However, in practice/experience the effect is not very pronounced. If I was concerned about it because of general moisture in the area,  then I would use zinc paint between the joists to help reduce any mold issues.

If spacing is preferred, then I'd recommend a 1/8" space (similar to the space between roof sheathing/plywood). There might be some kind of special spacer, but chances are, it's a rare and unpopular product. You could potentially use washers, but that could be tricky unless you use bolts (I would want the nail to go through the washer to keep the washers from falling out). 

Another way that this could be accomplished would be by using steel or aluminum shims. I would just cut my own from a piece (or three) of 1/2" x 1/8" steel or aluminum stock... maybe 6 foot long, and use 6" strips as spacers.