That myth again. You do not instate referenda for laughs. They are bound to laws and constitutions as well and the national government/courts/parliament might have leeway on when a referendum is necessary.
More importantly those referenda were about adjusting national constitutional issues that would have prevented the implementation of the EU treaties, they were never held about the EU treaties because the later are international treaties and are constantly handled by the government and parliament. If you then remove or reshape the treaty segments that make a constitutional amendment necessary the legal basis for a referendum goes away.
Overall a EU empowerment through a europewide referendum would be nice, but since people have trouble with their own political systems I can't see that from not getting hijacked besides the point. The absurd play is that on one side the EU is decried as undemocratic but on the other hand eurosceptic countries will do anything to prevent a democratic EU since it would empower the EU government to enormous degrees. The EU constitution was partly shot down because it would have given a lot of power to the EU parliament.
Luckily the EU treaty of Lisbon still transferred alot of new oversight powers to the EU parliament so that development is positive. What they still lack is shaping legislative policy by themselves and budget control.
But once again the undemocratic machinations of the EU are actually in there because member states want to prevent a democratic and hence far more powerful and independant EU government. They do that by giving a commission the directives of what to do and maintaining control via the EU council and by withholding budget and legislative rights from the EU parliament.
Of course, a supranational government with the democratic legitimization to exercise its powers would necessitate constitutional amendments in pretty much all EU countries (e.g. the supreme court in Germany made it pretty clear that the German parliament is the highest government body so to give sovereignty to another entity would require a change of the constitution)
It's a merry-go-around of one leads to the other which is the reason the state of the EU institutions is in such limbo and it is very precarious of giving it new powers.