Your washer may not disappeared. It may have just stayed stuck in place.  There is a brass tube that threads in from the upper side, that the needle runs through, and if you don't have the washer in place your main jet may be pushing up on it. I would also think that if the washer was not there it may affect the way the needle seats, but if it's running good, and you don't think the main will back outyou probably don't have anything to worry about. Stay safe while enjoy your bike.

This subject has me wondering if a thicker washer , or another thin washer used in conjunction with the stock main jet washer would have the same effect as raising the needle ?  I know that most, including myself have done the white spacer mod, or similar, but I was just wondering if basically lowering the main jet was about the same as raising the needle.

The washer prevents the needle jet from lifting up and keeping the needle from metering the flow.  Changing the thickness of it won't have an impact.