Since the protocol should be the same (I refer to the ultrapeer protocol) there is no problem connecting to Gnucleus, Aqua or Lime (Aqua is made from the same source as Lime, but with some enhancements; BTW, MamiyaOtaru is who makes these versions, and he is doing a great job
).
Lately I have seen more connections to Gnucleus ultrapeers, and I get the same search results. The only difference is that if you connect to an "old" peer without ultrapeer protocol (Lime 1.9 or earliear, Phex -if they don't have the ultrapeer yet-, and some others) you'll need more bandwidth, since the Gnut/0.6 protocol uses more bandwith, but there isn't a real reason to ban them (IMO).