EW, stop calling the people stupid.
People, stop being stupid.
*rimshot*
No, but seriously, folks, lets discuss this...
We know that cloaking was developed during Wing Commander 1 -- it's mentioned several times in Super Wing Commander, and the first use of manned cloaked fighters was in 2656, just two years later (note that I am not referring to Wing Commander Academy -- that was *not* the same type of cloaking... that was more akin to the Shroud Device seen in WC3). In fact, Super Wing Commander deals with a fight between Halcyon and Tolwyn regarding the existence of stealth fighters -- why would Halcyon believe they exist, had the Kilrathi not already been working on the technology?
Anyway, if they could cloak a living organism in 2656, it stands to reason that they could partially cloak a missile in 2654 -- especially since we see it. We also know, thanks to the movie novel that it was a prototype -- this is further explained in the Confed Handbook. The handbook also specifies the model number, and some operating details... so we know that it is *not* the same type of Skipper being tested in Wing Commander III. (Note Eisen's line... the Kilrathi were tested a *new* type of cloaked missile... no indication that it was the *first* type of cloaked missile).
As for Blair and Sosa, it's specifically stated that they do *not* have an affair -- we also see in the video sequence s of WCIV that Blair *is* interested in Sosa (he comes on to her when she's doing the data translation by hand, and is later shocked that she's hooked up with Catscratch in the veggies scene).