So, first let's look at the genuine issue which has probably caused you to be concerned, put a number on it, then look at the arduino numbers.
Triggering instruments over MIDI, which is a serial protocol at 31250 baud with 1 start bit, 8 data bits and 1 stop bit, but no event clock worth speaking of, can introduce audible effects. To send 12 'simultaneous' note-on messages each of three bytes, takes
10 * 3 * 12 / 31250 = 11.5 ms.
That will be clearly visible on a scope in terms of transient smearing, may produce phase cancellation effects and may easily be audible.
Now lets look at sending two port out instructions, at a 16MHz clock, and to be charitable lets say that is 4 machine instructions (it is probably one but my connection in this hotel sucks so i can't easily check right now). The delay between the first set of 8 triggers and the second set of four is
4 / 16000000 = 250 ns
or 46 thousand times less than the MIDI delay. Or to put it another way, if your DAW is running at 96kHz sampling rate, the delay is less than 1/40th of one sample.