Hi Pat,
A possible source for the hardware you are seeking may be a well stocked electronics supplier, like Radio Shack in North America. In the past, they had a good selection of fine thread nuts and bolts in various sizes, but I don't know their current inventory status. Another source may be an upper end model railroad parts supplier, in the past I remember a brand (Grant???) with a line of very small precision brass hardware - some being very small.
To better illustrate what I did, here are some photos:
The first shows the bolt just by itself passing through the hole in the deck and threaded a few turns into the nut under the deck. The nut was secured with a few pieces of styrene and superglue before the deck was cemented to the hull. This is a simple rig intended for a minimum of threading and unthreading only - it is not a robust design, just enough to secure the conning tower properly in place without using any adhesive.
This next image shows the bolt fully threaded in place with the conning tower (still in primer). A thin nylon washer helps to more evenly spread the pressure of the bolt to the conning tower.
The last image is of the set up from above. The head of the bolt sits flush with the deck and will be covered by the periscope housing.
I still need to fill in the old Amati conning tower outline in the brass deck as it does not exactly conform to the modified Revell conning tower footprint. I think I will try some very thin styrene strip and superglue, then carefully sand it level with the rest of the deck.
Cheers,
Bill