Andy, try Googling for a map making program called Hexographer. I believe it's under ongoing development. It's fantasy biased, but the developer is open to scifi suggestions for symbols and was planning to make symbols customisable. I dunno how far down that route it's got, but it might be worth checking out - it's gotta be a year since I last looked at it.
Obviously, if the symbols you want are Traveller copyright, he won't be able to provide them, but if the custom option is there now, you could make your own.
Other than that, if you can import the hex paper into a graphics program and then draw your symbols in PNG format with a transparent background, you can paste and move them where you want. I might be able to talk you through the process if you have graphics software I'm familiar with.