Probably not because there are other scenes where flashing lights were used to communicate information, and Morse code assuredly would not have been used there.
I do not know Morse code, but I would still reason that this scene most probably does not use it (and if it did, I would consider it a plot hole). This is because there are other scenes in which flashing (strobing) lights are used, and where there is no reason to use Morse code. These scenes occur within the ship where we are in a "100% alien environment/situation". And it occurred more than once (could not find YouTube clips):
- Immediately after the scene in the question, Klaatu orders Gort to stand guard while he goes into the ship in order to program a global blackout. We see strobing lights as Klaatu speaks in his native tongue. I am pretty sure that he was having a dialog with the ship. That strobing light was most definitely not Morse code.
- After the classic "Klaatu Barada Nikto", Gort brings Helen into the ship. Now Gort has a "dialog" with strobing lights. We can be 100% sure that Gort understands strobing lights, and we see that light within the ship communicating with Gort -- not Morse code.
- Something similar happens after Gort retrieves Klaatu and performs a medical procedure to revive him.
I, for one, firmly believe that these strobing lights are a language that is not from Earth. Klaatu is not using Morse code, but his "strobing" in not nonsensical; He is giving orders. If you recall, once Klaatu was in the clear, he very authoritatively spoke an order to Gort -- probably to guard the entrance to the ship.
What is Klaatu telling Gort?
My interpretation: He is ordering him to make the way clear for him to enter the ship incognito.