Given the fact that Windows phone is incompatible to Windows...
... I doubt that. Windows CE at least had the advantage that it was similar enough so you could port some applications or you could get a Visual Basic programmer (yes lots of commercial software was written in that) to write for Windows CE.
Now moving either to Windows Phone or Android means that you'd have to completely renew your software. Your old software won't work, you need to get new one. Companies will have to buy whatever they can get their software for. It's probably much easier for software companies to find Android programmers in the price range they can afford. There's just more of them around. Plus nobody knows if Windows Phone will be a long term strategy by Microsoft or yet another flash in the pan. Android seems like something that will be here to stay, at least for the next 10 years, so it is worth a bit of investment. Nobody knows if Windows Phone will even exist in 5 years.
Microsoft could have gotten it so easy, by just porting a stripped down version of Windows to mobile phones. They could have built a x86 emulator just like the one they had on Alpha (OK that wasn't done by them) and you could have gotten all the normal legacy Windows software to run. With that they would have gained that market in a flash. However that would have meant to acknowledge that Microsoft is mostly about legacy software.
Some people may find it bizarre, that people who run old Unix shops can just sit back and relax. They probably already run terminal servers for over a decade, and adding a mobile device just means installing some ssh client on it. (or mosh if you want to use it over GPRS)