Unless more complicated things happen inside the column, the width of most peaks is about the same when they approach the column exit, independent of the retention factor. Ignoring peak compression in gradient chromatography, the same is also true in gradients - the peaks are of the same width as in isocratic chromatography. If I would be able to measure the peak width inside the column, I would have no problem measuring plate counts, independent if I run gradient chromatography or isocratic chromatography. I would measure the width, divide the column length by this width, square the number, apply a factor that depends on how I measure the width, et voila, I got the plate count.
The problem with gradient elution is that I can not relate easily the width that I see on the computer screen to the width inside the column. Therefore the width that you see on the screen can not be used readily to count the plates.
The only thing that you can be reasonably certain about is the fact that you have more plates in your column than in your kitchen.