I have a depression in my OSB floor caused by a layer of rot
A 3x3 repair using the technique you describe is just fine, assuming that it's not in a critical location, such as immediately adjacent to the toilet drain opening. If it is, you might find that the stress of the toilet on that spot results in too much flex. In that case, cut the area out and float some lumber under the patch edges and replace the piece. 

Otherwise you're unlikely to have a problem. Thinset mortar won't provide much stiffness, but it's certainly hard enough to  do the job.