If a ship is over-extended for some reason or is off chasing a single frigate across the map, a significant delay would most definitely make an impact. The timescale of combat compared to 'real' time in-game is likely disconnected from the gameplay, so an order that takes 2 seconds of IRL time may take a lot longer for the crew and command to 'actually' execute. Gameplay first, THEN the lore can be used/changed to justify why things work the way they do.
Ships should definitely be responsive to orders. A queue would kill an already under-used feature. Latency on a per-ship basis may work, but it would still needlessly complicate an already quite complex game.
I think the most important thing is to refine how orders are actually carried out, with ships not acting suicidally whenever an attack order is given, and 'Avoid' command not creating a ridiculously large area that your entire fleet will avoid. Perhaps make Avoid based on the enemy ship's weapon ranges?
Edit: #1 thing I want related to commands is for escorts to take cover behind their escort target to vent flux if they're being overwhelmed. Escorts are useless because they so willingly facetank everything. If I have a decent fleet vs. anything that may pose a risk to a good frigate, if an escorted ship presses the attack then those escorts will almost always die. Good escort AI would make frigates really useful.