I have often pondered the same question and I did a test to see if this where the fact.
Ultimately I found it is a matter of confidence, given that I was taught that the base of the bullet is the most important part of the bullet, I prefer to have mine as close to perfect as possible.
I have shot them with the bump from the sprue in the base, without the bump, tapered, bumped and just about everything inbetween without a real noticeable increase or decrease in accuracy. If the bullets are all the same, then they will go into the same group.
I did discover during this what causes the bump from the sprue. It is the manner that the sprue is broken with. Many have some sort of mallet and give it a quick sharp smack to break the sprue.
When you do this and it results in a bump in the base of the bullet, it is because you are hitting the sprue on a downwards angle resulting in the sprue bouncing upwards from it hitting the top of the mold instead of being broken parallel to the top surface of the mold. This will also cause the top surface of the mold to gall, especially in the aluminum molds such as LBT or Lee. This can also bend the sprue and result in bases that are cockeyed.
I break all of my sprues by hand pressure where I can. This is mostly 2 cavity molds that are made of Aluminum, but I do the same with some of my RCBS, Lyman and SAECO molds.
This is the reason that Lee has the sprue handle on their molds and is also the reason why Veral designed his sprue plates with the angle on the sprue plate.
Now I have a minute if any bump on my bullets.
In addition I will say that I have altered the ejection pin in my lubersizer die. The stock die ejection pin has a dish in the top of the pin, I had mine ground perfectly flat after I noticed that the bottom of the gas checks had a convex instead of flat base.
Now I cant say to what degree all of this will affect accuracy, but it does wonders for my confidence knowing I have done all I can to make the bullet base as close to perfectly flat as I can.