CR2016 cells are indeed 3V. The “CR” code denotes a lithium manganese dioxide chemistry, nominally 3V.
Alkaline button cells are 1.5V and are given “LR” code. The typical form factor is also fatter and taller than lithium coin cells.
A pair of CR2016 cells shouldn’t be any concern, but because of the low forward voltage on the Yuji’s, they run pretty well on a single CR2032 cell, in my experience.
I haven’t done a controlled test, but I’d expect you would get more stable output and significantly longer runtime out of a single CR2032 compared to a pair of CR2016’s, although you might get higher initial output out of the latter. The massive voltage drop the pair of smaller batteries experience is in part due to a lot of energy being wasted on internal resistance.
Either cell does better at these kinds of loads with intermittent use (a few minutes at a time) than continuous use. It’s surprising how much the voltage recovers when a load was removed in a test HKJ did: