On the 990, the reason was part performance and part cost. By having DVI switching that was a pure pass-through, they didn't "muddy the water" and they reduced the likelihood of HDCP problems. Additionally, implementing the video processing required to generate a menu signal (even if it just replaced the incoming signal) would have been quite pricey in 2004 or 2005 (and the 990 launched in May 2005).

These days, we are seeing a lot of new offerings that can output their menus over HDMI. Part of that comes from the inclusion of high-powered video processing systems that are converting analog to digital and doing lots of digital video processing, as at that point they can generate one menu (in the analog domain so it can go onto analog inputs and be visible at analog outputs) and let the video processor convert them to digital along with the other signals. In some cases, they may even be overlaying data onto HDMI inputs, although I was turning that sort of stuff off back in 2002 when it was available via s-video switching on my 950 so I haven't paid much attention to that.