There are several reasons that probably played together
First, the Wagenburg was a device of asymmetric warfare, that proved effective when first used against Crusader and Holy Roman forces, that still mostly relied on heavily armed knights, and were arrogant enough to charge head-on.
Later the asymmetry faded away as these tactics became more or less prevalent in the region – for example some Hussites changed sides and supported Emperor Sigismund, while others became mercenaries (for example in the army of Corvin Matthias in Hungary – and this immediately decreased its usefulness: Two wagonforts set up on opposing hills and trying to trick each other into opening the circle or trying to starve each other do not represent a particularly efficient way to decide a battle.
Simultaneously, the enemies of the Hussites learned tactics that could sometimes be used to defeat such wagons: See the Battle of Lipany again.
Secondly, as field artillery advanced both in mobility and firepower, it would have meant more danger to the wagons. Wood is a credible material to be used against arrows or contemporary small arms, but can not absorb cannonballs the way earth ramparts can. It will burst into deadly fragments, as the poor sailors of 18th century warships had experienced. So if your plan is to sit in your camp and weather the enemy charges, but the enemy sets up a powerful battery on the next hill, you are dead.
Thirdly, the type of armies that used the Wagenburg – namely mercenaries and religious fundamentalists, recruited mostly from lower class burghers and peasants, and sometimes gentry – had by the end of the 15th century developed a much more effective tactic: dense pike (and shot) formations These were almost as cavalry proof as the wagonforts, while they were much more mobile. They could actually charge on the field and they could be disassembled to much smaller pieces (individual landsknechts). So they could pass on any kind of terrain (including in siege trenches) and then form up as necessary. Look at how Marignano was different from battles a century earlier.
Other countries, namely Poland and Hungary, where the wagonfort was introduced, later lost their strong royal authority, while they developed the highest percentage of nobility. Without strong kings, they could not afford standing professional armies, and their poorer nobles preferred horseback fighting. Hussars emerged. (whose etymology is uncertain, but has nothing to do with Hussites ) So the Ottoman wars in Hungary after the disaster at Mohács (still fought with armoured knights) consisted of sieges and raids. On raids, the wagons are a hindrance, and they are not needed during sieges either: The besieged have better fortifications already, while the attackers are usually so overpowering, that they need little defense, or they have plenty of time to build proper contra- and circumvallations.