I have some experience in a school research with hydroponics in tomato (Lycopersicon esculentum). Pests attacked similarly to the plants of different hydroponic treatments than the plant with the common method of cultivation. But we no tested directly if there was a difference in the herbivores between plants with different treatments.
Typically hydroponics and aeroponics are deployed in controlled environments (greenhouse, growth chambers)), which tend to have lower pest pressure than that of field crops for either systems (easier to exclude pests). I doubt that there are any distinguishable differences between the two systems for insect pests -- none in my experience, but I have not published or come across literature that addresses this... it may be out there, I just haven't looked all that closely.
In terms of plant pathogens (bacterial/fungal) then there may be some differences depending on the nature of the water loop that you are using and the type of hydroponics you used (NFT, deep trough, etc.). Regardless of the system used I would recommend a disinfection step, at least for the recovered solution (assuming you are recalculating the water).
Not sure if this helps at all, but you may be on to a good question to conduct some research on!
Invasive alien plant species have become
dominant components of many landscapes, where they
are indicators of ecological disequilibria. They coexist
and compete with native plants, disrupting a wide
range of trophic interactions, and must cope with a
new array of herbivores. We examined factors influencing
the occurrence of invertebrate herbivores...
We report Paricá as the first host recorded for Mysaromima liquescens Meyrick, and the damaging potential of M. liquescens larvae as borers in Nova Canaã do Norte, state of Mato Grosso, Brazil.