If you're thinking of buying plastic sheets and silicone and or shellac, just save the money and buy a sheet of plywood then cover it with a table cloth.
The plywood will provide stability as well as prevent liquids leaking through the slats to the floor, etc. A thin coat of sealant will provide at least as much waterproofing as any other wooden table has.
Not seeing or knowing the length of the shelves you are using, I would not use slats to assemble the top. It would be another expense saved. I would use a cross layer of selves for that if there were enough of them and the table was small enough, since this material sags readily under its' own weight. It will make the table heavier, but it is not like it ...
Your most "microbe resistant" option would be what you already thought of: a thin plastic sheet. Just glue it down with contact cement, rather than drilling and screwing, if you are worried about the screw holes (I would not be so worried about the screw holes myself...)