Nope. I think this is one nuance that you should not be so picky about it. The symbolism is more for the player to recognize. If any other symbol was used, one would naturally be confused as to what it means without further explanations. However, when you get the iconic pirate symbol, you immediately recognize that these are indeed pirate ships without needing details, and that your weaker ships should stay away.

To assist your suspension of disbelief...

Not all pirates are humans but all known pirates so far are humans with the occasional alien recruit. Piracy is apparently a natural occurrence among humans, not so much with aliens.

The emblem is a skull not a skull and crossbones. The skull has been used by humans forever as a threatening icon. Hitler's SS is an example.

You have to work at it.  

The actual reason is that the player is a human and can recognize the symbol on an iconic level, but that is boring.

I am not buying that the other races had to learn piracy from the Terrans, especially not the Drengin.  However, I can envision humans being so naturally good at it that their historic icon, an abstracted skull from the original and forgotten Jolly Roger, has become adopted as the galactic symbol for piracy.  That makes all too much sense, really. 

Are you sure those aren't Altarian skulls?  They look Altarian to me. 

Arr ... invent your own symbol, matey!

I guess it would be kind of interesting to design skull-symbols of the different races in GalCiv.