Have there ever been any accidents within holding stacks?
The article you linked in your question mentions one incident - loss of separation - that's described in more detail here.

The Aviation Herald is a good source of information on incidents and accidents but it has very few reports related to holding. There are several about low-fuel incidents because aircraft had to remain in the hold for a long time (Avianca 52 is a well-known case), but I could only find one that involved a holding pattern more directly and that was also a loss of separation resolved via a TCAS advisory.

Eastern Airlines 401 crashed while in a hold, but it was an ad hoc holding pattern and not in a stack with other aircraft. American Eagle 4184 crashed due to icing accumulation while holding but again there were no other aircraft involved.

I could only find one example of an actual collision in a holding pattern which was over New York in 1960 and in that case only one of the aircraft was holding (inaccurately).