Well...tbh i dunno but have thought about it to myself quite a few times before, excellent topic. But the statement that no humans exist within the PMD universe at all isnt exactly the case due to PMD2. Anyway thats beside the point. I beleive that the pokemon know of humans but havnt had much contact with humans posibly due to them being in seperate dimensions :/ ? And the knowledge that humans exist could come from pokemon with extended psychic sight like Xatu, or from spacial pokemon such as Palkia. Idk.
Or a little simpler, maybe humans just died out somehow or became so exceedingly rare that you just really dont see humans at all(ironic huh?). What do you guys think?