Will (assuming perfectly, or almost, considering we're humans)clutchless shifting your car all the time affect in a worst way the shifting box mechanism than shifting the gear in a regular fashion, using the clutch?
The clutch is there for a reason.
It's true that some drivers, with some cars, can shift a manual transmission smoothly without it, and it's a useful skill to have in an emergency (if the clutch fails such that it's always engaged, and you can keep from having to stop the car, you can keep driving). However, when you do this the synchronization gears ("synchros") take a beating, as they shoulder all of the work of bringing the transmission gears to the correct speeds depending on road speed and crank speed.
Disengaging the clutch ("putting it in") and then gradually engaging it ("letting it out") as you shift lets the clutch disc take most of the wear, instead of the syncros; as the clutch engages, friction on the disc forces the input shaft of the transmission to match the crank speed, which in turn sets up the syncros to bring the main gears inside the transmission to the correct speeds before they meet.
So the short answer is yes, no matter how good you are at shifting the transmission without the clutch, you will cause premature wear on it. A clutch is much cheaper to replace than a transmission, so it's better to use the former whenever possible. Put the effort you are putting into practicing clutchless shifting into learning to properly match engine revs when downshifting instead—this is an increasingly forgotten skill that will give you the biggest payoff in terms of reducing wear on the car (and make your driving much smoother!)