Clutchless shifting, when done correctly and smoothly induces almost no stress on the engine, clutch or gearbox. I almost never use the clutch upshifting and only about half the time downshifting. Nearly all semi drivers seldom use the clutch.
Long term effects? It depends on how you do it.
When I first started riding I usually used the clutch to shift, but felt there was a better way to do it. Once I started to riding on twisty roads such as GMR I stopped using the clutch for upshifts and have been doing it ever since. I must qualify that by saying I use the clutch to downshift most of the time to prevent excessive engine braking when setting up for a corner -- slipping the clutch helps keep the rear tire hooked up under hard braking.
In the 40 years and well over 500,000 miles of riding hundreds of different motorcycles I have not had a trans failure due to wear or damage from clutchless shifting, and I tend to hang on to bikes for a very long time -- my '88 Honda Hawk GT, which I still have, has right at 150,000 miles on it and the notoriously weak trans was doing fine until a crash in a diesel fuel slick jammed the shifter hard enough to break a shift fork.
A quick overview of the internals of a typical motorcycle trans drafted on my CAD program:
Gears engaged. As long as there is a load from accelerating, decelerating, or steady riding the gears are locked together.
Disengaged. When the load is interrupted either by rolling off/on the throttle or pulling in the clutch the engagement dog faces lose contact and the sliding gear is free to move. It takes very little time for this to happen.
Blocking happens about 60% of the time when engaging the next gear regardless of whether you use the clutch or not -- the shoulders of the dogs meet and have to slide scross each other to drop into engagement. This can be felt as a "step" in the travel of the shift lever.
This blocked condition is when most damage happens. If too much force is applied to the shift lever, the film of oil between the shoulders is pushed out, resulting in metal to metal contact. As the dogs slide across each other the contact area decreases and wear increases, reaching a maximum just before they clear enough to engage, rounding the corners. Once there is enough rounding the faces will become angled, eventually pushing them apart with sufficient force to overcome the tension of the detent, causing jumping out of gear usually under hard acceleration, but eventually all the time.
In order to prevent this, apply only enough pressure to the shift lever to move it (plus a little) and keep this pressure applied until the next gear is fully engaged -- the false engagement of the blocked condition can feel like full engagement, but if you let off the shift lever at that point the only force completing the shift will be from the detent roller, which is insufficient and will cause partial engagement or skipping/grinding.
Shifting without the clutch will not cause any more wear than with the clutch as long as you learn how to do it properly, and with experience can make shifts practically undetectable other than a change in exhaust sound.