Yes. If more than 50 messages are sent, MIDI Designer will pause for .1 of a second (100ms). This was to solve two particular user scenarios (where the target was getting overloaded) and worked perfectly. We haven't seen a situation in which this doesn't work, nor a situation in which the latency is too great.
Update for 1.6.1 (still in testing as of 2014-02-21)
Now the pause is .01 multiplied by the number you have in the Throttle setting in Config. MD sends 5 messages per batch. This seems to keep the JD-990 happy.