I think the 'X is the Doctor!' covers appear when their first episode is broadcast - for example the 'Peter Davidson (sic) is the Doctor!' cover was on issue 61, however Davison first appeared 6 months before on issue 55 (which was 'Introducing Peter Davison').
Colin Baker's first appearance was on issue 88 (which was his 'Colin Baker is the Doctor') cover, while McCoy's never got an '...is the Doctor!' cover - his first issue was 124, which just had the caption 'The New Doctor'.
McGann's first cover was issue 236, and Eccleston's was 342, both when they were revealed, however given the lack of TV broadcasts at the time, it's not a surprise that they got a cover straight away. Finally Tennant's first cover was issue 359 (the ..is the Doctor!' cover), however this was after Series 1 ended.
So on the whole. although most Doctors' first appearance on DWM was their '...is the Doctor!' cover, at the same time you'll notice they were never introduced as the Doctor until they had actually taken over (with the exceptions of McGann and Eccleston, since when they were announced there was no incumbent Doctor on-screen). Plus there was the whole Davison issue, who never got a proper '...is the Doctor' cover until issue 389, thanks to the infamous foul-up in 1981
The problem with Smith is that there will be a year between his announcement and his actual taking over the role. During that time it would be very unprofessional of DWM to jump out with a cover saying Smith is the Doctor, when until 2010 Tennant will still be in the role. No doubt whenever Smith takes over on-screen, then DWM will come out with their 'Matt Smith is the Doctor!' cover.