As it turns out, there actually are set percentages for item spawn on each floor of a dungeon. I was able to find what is essentially a text dump with the deep information on each dungeon, including the rates of spawn of items, traps, enemies, etc. [I have no clue how the original creator(s) found any of this--presumably they dumped the rom].
The link is here:
I apologize for the general untidiness of the page, but the information is very helpful and interesting. Perhaps someday it could be organized into a more interactive guide.
As a side note, I'm not sure who maintains the PMD Explorers Wiki, but their fledgling site could really take off if it had this info organized into pages. It could also be a new host for the Wonder Mail S Generator and other informative and helpful guide services that have had their domains expire in the past few years. I have had trouble finding solid info on this game, and I think we need a single site where we know it can be kept safe. If anyone would be interested in helping to transfer this information over and categorize it, please let me know!