But to be fair, I will be much more specific.
Please answer:
1. If players have line of sight (which they have) they can enter/exit level 1 Rotten Halls with Misty Step.
2. Players can polymorph themselves and enter/exit Rotten Halls.
3. Players can polymorph themselves to creatures with enormous strenght and literally use axepick to force through stone.
4. Players can use gaseous form to enter/exit Rotten Halls on demand.
5. Create Zombie/Skeleton gives PCs giant advantage on traps discovery/overcoming. How you would deal with a wizard with small army of zombies?
Thanks in advance.
1 & 2 & 4. Cover the outer boundaries of the Tomb with an undispellable illusion that there are no cracks.
Once the party has entered once, gathering puzzle cubes is no longer fun, and circumventing them becomes a relief, not a bug.
3. Unlike previous editions, rock can't be trivially mined through (in d20, it was just a matter of inflicting enough hp damage per cubic square). Have the Yuan-Ti investigate if they set up a day-long mining operation. If this warning doesn't deter them, have them launch a coordinated assault together with gargoyles and every Tomb guardian that can reach the entrance with the intent to TPK them for being too slow.
If the combined mass of enemies aren't enough to win the day, the party is over-levelled.
For each significant ally they bring, you're free to add the corresponding reinforcement to the bad guys. Ideally making the good and bad NPCs square off against each other so you don't have to run that fight in detail (just roll a d6 to see who wins).
5 & General: If the party feels trivializing traps by endless summons, I'd let them. They clearly want something else out of their D&D gaming. (A dungeon that consists mostly of death-traps might not be up their ally, however.)
The point is that D&D is a game that assumes the heroes want the heroics for themselves. Applying realistic tactics and risk-mitigation strategies only work to lessen what makes D&D fun.
The players need to be aware of the fact they're expected to WANT to walk in the footsteps of Indiana Jones. Not merely dealing with his challenges, but actually solving them his way - taking reckless risks, gasping with delight, narrowly averting certain defeat.
It's neither your nor the module's job to anticipate and counter every little thing players may come up with, if made in bad faith.
In the end, if they don't want what D&D offers, no in-game solution will work.
Maybe your group is even burnt out on role-playing? In which case I suggest you switch things up for variety, and to get your appetite back. Try a dungeon crawler board game for a change. I've heard great things about Gloomhaven.