I'm fitting hardboard on my bathroom's floor in order to glue vinyl on top of it. However I'm using 2 kinds of hardboard. One is 3mm thick, and the other 2mm. Is this a problem, and if so is there an easy solution for it?
I don't think using two different heights is a good idea. For one, you'll introduce water pooling, depending on where the heights vary. For another, you're ensuring that the vinyl is always under the risk of stress where different heights meet under the same sheet.
The easy solution is to use only one height of hardboard - stick to either 2mm or 3mm.