The latency of the audio buffering in the FX chain is, as you say, dependent on the structure of the chain. We intend to add a feature to fix this latency because this will make DAW integration easier. At the moment, we keep it to the minimum possible given the configuration.
Some algorithms have inherent latency in addition to the buffering latency. So if you ping, you might find the overall round trip latency changes depending on which algorithms are loaded, even if the structure of the FX chain is unchanged.
Since our algorithms do not "know" or have a way to report their latency, we currently do not compensate for this inherent latency – so with these algorithms, you can potentially have issues if they are run in parallel with other algorithms, or if the master mixes on the algorithm and FX chain are not 100% wet.
The right solution to this is to test and analyze all the algorithms for their inherent latency and provide a way to report this to the H9000 hosting system, so that it can adjust the FX chain latencies accordingly, but this is not a simple task!
I looked at Omnipressor (1116) and it looks like it adds a fixed 0.5ms of inherent latency.