I do on my Lowa Hunter GTX Extreme boots. I like to give them treatment after 6 moths or so to help keep them waterproof, treating and conditioning the leather even though they have Gortex. Using a product similar to LOWA Water Stop seems to work well for me.
I treated them right out of the box from day one and it's help keep them in great shape for multiple seasons now.
Usually treat leather boots before I wear them in the field or off trail by the manufacturers recommendations or email/call the manufacturer and ask them if a particular product is safe on their product, most times they are knowledgeable. My "daily drivers" I that are fabric and leather I wait until the factory DWR has worn off before treating as stated above.