Latency is an issue in certain scenarios, though you can compensate for it in a number of ways.
The other night, I was generating a sequence in Reaktor for a hardware oscillator to A/B it against a Block. I then brought the oscillator back into the computer to treat with Reaktor's LPG. The LPG was plucked by the Reaktor sequencer's gate.
Because of the latency, the note changes on the oscillator were late compared to the LPG's pluck. I compensated for this by inserting a Gate Delay Block between the sequencer and LPG. After that, it worked perfectly.
It's not an ideal fix, although my patch was an unusual use case for sure. If I sent the sequence AND gate out of Reaktor and used it to trigger an external LPG, there wouldn't have been any issues. Generally, if you're just going in one direction (modular controlling Reaktor or Reaktor controlling modular) you won't have an issue.