Yes, the 40ml edition is released from time to time; the last time of which was around Xmas 2005. I know this for a fact, as I was working with Parfums Issey Miyake at the time.
As long as the cellophane wrap is still intact, I doubt you will have any reason for concern. Its a handy size to have.
EDITED TO ADD:
Just keep this in mind: if there is a thin dark blue stripe on the front of the box, separating the silver and white panels of colour, then this is fresher stock than Issey with a wider, metallic blue stripe between them.