Between 97 and 05, the MVP votes Duncan and Shaq got are as follows:
98 – Shaq #4, Duncan #5
99 – Shaq #6, Duncan #3
00 – Shaq #1, Duncan #5
01 – Shaq #2, Duncan #3
02 – Shaq #3, Duncan #1
03 – Shaq #5, Duncan #1
04 – Shaq #6, Duncan #2
05 – Shaq #2, Duncan #4
Assuming that your 5-6 les estimation was sincere, you are talking about the pair winning about 75% of the available championships together between 98 to 05. Duncan was better in MVP voting in 4 of those 8 years, and it would hard pressed to say that Duncan will not be able to win at least one regular season MVP in those 8 years.
Also, Duncan not being ego-driven doesn’t mean he is not compe ive. If the team structure requires Duncan to step up, he will, and I believe Phil Jackson, or any other coach would have ran the offense through both Duncan and Shaq, with Duncan manning the defensive area on those teams.
That said, I don’t think the team would have won that many championships, a big man needs a guard, not another big man. Kobe was playing his second fiddle role very well in the 97 to 03 time frame, unless the Lakers got a decent PG, and a couple of shooters, I don’t see the Duncan Shaq combo going past the Kings and Jazz with regularity.
EDIT: Also keep in mind that with Duncan in the middle, Shaq will probably go company time more in the regular season, further undermining his chances, and boosting Duncan's chances, at the regular season MVP.
As for finals MVP, tough to say, who would have thought Worthy would ever win a finals MVP, or Cedric Maxwell?