Making the handles thicker, may require a little heat re-molding of kydex sheaths or re-wet-forming of leather after you find the overall thickness that fits you usage best.
I was evaluating that very issue yesterday -- thinking that if I was able to increase the thickness of the scales, the kydex sheath would need re-molding.
It all depends on specifics of how the sheath fits. I'd recommend focusing on making the knife handle fit your hand under extended use.
Reforming the small area of kydex is fairly simple process. Localized heat to kydex, insertion of knife (with tape applied to handle area - to create desired fitment security) then press molding through the cooling process (with couple towels on each side under pressure).
Consider also the factory ESSE plastic sheaths most likely will fit after increasing liner thickness, and they can be bought cheaply (I actually prefer the factory plastic to kydex for my applications, AND did NOT need to remind sheath after installing liner).
Additionally, you may need longer Chicago Screws depending on thickness increase (less than $1 at my local hardware store). As I referenced above, I chose to only do the palm-side and was able to reuse the factory fasteners. I found 45-mil sheet rubber (for liner material) to be good thickness increase, and the rubber just slightly bulges proud at the exterior gap (when screws tightened) providing a really nice grip and feel. I have 45-mil and 60-mil sheet rubber for various applications.
I did my ESSE-6 first, then ESSE-3. I found same thickness, liner palm-side only, to work on both knife sizes.
Again, I would recommend focusing on the handles b4 worrying about sheath fitment (or just order up an inexpensive ~$15 factory plastic sheath - you might find it's actually much better than your read about ;-)
Additionally, aftermarket handle scales can be bought. For me a simple liner-mod to factory micarta was best option.
If you feel you want any help, let me know (up to & including doing the mod's 4u & possibly re-profiling the edge, etc.). Happy to assist any way I can.
Regards,