This issue is related to privacy not "bad crypto" or math.
It's bad crypto alright. Monero users were transacting "anonymously" for a year only to discover later that they could be trivially deanonymized because those in charge hadn't fixed a "hole" in the system from the start.
As to the InstantX jamming theoretical attack:
The attack vector on InstantX was about the attacker owning hundreds or thousands of masternodes (ie paying tens of millions of USD to acquire them) just to ...jam a InstantX transaction, which, if failed, would go as a standard transaction.
So, the game theory of the attack vector is that someone will pay tens of millions of dollars to jam an instant x transaction, while undermining his money in the process.
Do you see that the game theory of the attack vector is completely broken in terms of costs to the attackers and gains for the attacker?
That's elementary logic right there.
It would be like saying "bitcoin is fundamentally flawed because someone could buy 51% of the mining equipment and attack it". Yeah, well, if they did that, their equipment would then be useless. It's an economic suicide for the attacker, so to speak. The game theory has to account for this, no?