Right but that's not removing their effect. up until recently when Steemit only showed the top 50 on the witness page (now top 100) getting your name in the top 50 was a huge advantage as people would vote for you a lot more than witnesses outside the top 50.
Firstly, voting for a top 50 was much easier press a button and done.
Secondly by being in the top 50 the assumption was automatically that you had been vetted and considered a witness who was doing good for steem so people are more likely to vote for them.
To make it a fair comparison you'd need to look at what the witnesses ranks were prior to getting that vote and then model growth in their votes as a sub-50 candidate then a above-50 candidate and see how far they get.
Also I'm sure pumpkin is not the only ninja mined account. would be interesting to see what effect it would be to remove all ninja mined accounts.
I don't know exactly which accounts are due to ninja mining, but it is possible to identify some of them from the early blocklogs I have found.
If you look at the current situation where the witness voting page ends at 100, there is no significant jump above/below that point, but it could just be that we need more time for that to develop.
The longer the witness list on steemit the smaller the effect it will have. If you imagine a top 30 list (when everyone has 30 votes) the easy vote will be to just vote for the top 30 and there would be a big disparity between rank 30 and rank 31.
As you increase the length of the witness list the benefit of being on the page diminishes, but having had it for long means those who are in the top 50 have had a much longer time to enjoy the benefits.