Although I don't have as much interest in Sins as, say, a month ago, I find this a pretty interesting topic. I don't have any illusions that a) including a spy ship would drastically improve the game, or
that it will be included. However, as an idea, here's what I think:
I) The ultimate spy ship would be one that DOES NOT trip the "We Are Being Attacked!" message when it enters enemy space. The scout does a good job of being a spy ship as it is, but it trades stealth for speed, and offensive utility for helplessness. So...
II) The ultimate spy ship would have hidden functions, rather like the Q-Ships from WWII, or if you prefer the "phasmid" (specifically from the "Master and Commander" movie, but you see this tactic a lot in Patrick O'Brian's books). It would look innocent, like a contructor, a trade ship, or a basic colony ship, but it could "transform" into a heavy-weapon carrier. In this guise, it could carry LRMs, or a nice beam weapon, or planetary bombs, sneak in, and start to attack without immediately setting off the alarm. I actually would not envision this as a fast vehicle at all, but rather slow. It trades speed for stealth, and apparent helplessness for a hidden, focussed attack.