I can't believe I did it, but after Raw last night I decided to look into if Hornswoggle made sense as being the anonymous GM all along. Believe it or not...he kinda does.
1. In storyline, Hornswoggle was thought to be Vince's son for a time. This means they inevitably got to know each other, and perhaps even may have liked each other a bit by the end enough for Vince to believe he could run Raw. After all, after the last few GMs, such as Bret Hart, Vickie Guerrero, and a cavalcade of celebrities, he couldn't do any worse. Also, I couldn't find any time that Hornswoggle was in the ring when the RAW GM came calling.
2. Hornswoggle choosing to remain anonymous makes sense...being a little person, he knew nobody would take him seriously if he was GM. Also, at the time he couldn't talk, so the only way he could communicate is via email.
3. The part of him not being able to talk at the time does lead to plothole however, as when the GM was announced on RAW, there's a scene of Vince talking to him on the phone. This can be explained away, however, as Vince learning to understand Hornswoggle's grunts during the time they spent when he thought he was his son.
Of course, this does also reveal some interesting facts about Hornswoggle. For one, he for some reason never really liked Bret Hart.