When we talk about a joist, we have several forces at hand. Each end of the joist experiences an upwards point load equal to roughly one half the distibuted downward load.
These forces work on the joist to cause it to want to "arch" downward in the middle. These forces create a tension "stretching" force on the bottom of the joist, and a compression "pushing together" force on the top.
The "shear" force you refer to is only the difference between the compressive and tension forces at the top and bottom of the joist, but here's the catch. The closer you get to the middle of the joist, the less compressive or tensile force is applied.
The center of the joist does not have to be there at all, save the fact that it has to keep the top of the joist a consistent distance away from the bottom. There simply is NO compressive OR tensile forces at the center of the joist. The farther away from the center, the greater the force.
In fact, this is the key why a joist works the way it does. The effect of distance is exponential on the joist's strength. Pull out your span charts in the back of your carpentry book, and you will see that a 2x6 is roughly half as "strong" as a 2x8. A 2x10 is roughly twice as strong as a 2x8, and so on.
It is the distance between the top and bottom of the joist that makes it stronger, not the amount of wood in between them. Look at the engineered tussjoist systems of wood and waferboard and you will see what I mean.
A truss works the same way: The bottom chord is in tension, and keeps the top chords from pushing the legs away from each other. Other than a few intermediate boards in the middle to keep everything where it should be, there isn't anything in the middle.
Doing as you said, and removing material from the top of a joist, is equivelant to removing a block from the middle of a stack of blocks. The blocks are in compression, and removing one makes the rest of the blocks "push together."
Call any structual engineer you want, he'll tell you the same thing.