The word superannuation can and often is shortened to simply read super. In certain situations, when letters are missing from words, an apostrophe is inserted. In this case, am I correct in assuming that there is no need to add an apostrophe after the word super (i.e. super') to indicate to a reader that the letters "annuation" are missing? If am I correct, what is the supporting reason?

Good question. The best I can offer is common usage!

It feels more like an abbreviation to me than a contraction.

It's not that different from:

etc. > etcetera
public house > pub.

I could think of some more, but it's too early in the morning, and I haven't had a coffee yet.