Yes, the accelerometers were mounted on an optical bench and of course we could detect any minor earthquake (sensitivity was around 1e-10 ms^-2).
The bending of the floor due to the presence of people in the room was noticeble indeed.
For the accelerometers the problem was the tiny tilting of the sensitive axis in the gravity field. In this case you're probably right that this doesn't matter -
but in general it is difficult to rule out every second-order effect when the forces at play are so small with respect to g.
A caveat.
I had the change to perform a similar experiment at work testing very sensitive accelerometers. Believe it or not, the biggest source of errors was the bending of the floor due to the test masses!
A better setup would be to suspend the spheres exactly like the tuna cans, and test two configurations rotated by 90 degrees.