For very simple data, custom properties are ok (so long as you're aware that anyone who opens the file will be able to see, edit and delete them). And note that because PPT shares a common, too-small, allocation of data between links and document properties, adding too many of one can wipe out the other.
I'd use tags instead. Every shape, slide and presentation object can have a tags collection, containing one or more Name / Value pairs of strings.
These are invisible to the user and will not interfere with the hyperlinks in the presentation.
' To add a tag
With ActivePresentation
.Tags.Add "MyTagName", "MyTagValue"
End With
' To use a tag
If ActivePresentation.Tags("MyTagName") = "MyTagValue" Then
' Do something or other
End If