Warn about and deprecate element guessing in ITP parser

[IAlibay]

Behaviour post #3753

In #3753 element guessing is added to the ITP parser in order to partially guess masses.

Intended behaviour

Ideally we want:

1. To make sure users are aware of any guessing that happens
2. With 3.0+, remove any automatic guessing

Proposal

We add a DeprecationWarning on ITP element guessing that lets users know that this behaviour is happening, and that it will go away in 3.0.

cc @lilyminium