"Queuing twice for a cup of coffee is once too many." Is this correct?

'once' in fact means 'one time', and may thus always be used interchangeably.

Ordinarily one would prefer 'once too often' or 'one too many'. Often refers to time, hence 'once', where as 'many' refers to counts (or numbers if you will), thus 'one too many'. However, in this case you may argue that 'many' is better suited to accompany queuing for a cup of coffee than 'often', where as 'once' and 'twice' definitely sound more poetic together in the context, than do 'one' and 'twice'.

Thus you would be fine to write it, as you have in the title:

Queuing twice for a cup of coffee is once too many.

This is exactly what poetic license is for.

Those are all ok, although I think I like your first choice best:

Queueing twice for a cup of coffee is once too many.

One time sounds a bit funny to use instead of once, although there are places where it can work.