I see this difference when I'm working with lists in Data View Web Parts and manipulating the values in XSL. Why do some Lookup column values look like '1;#text' and others just have the text? I've never been able to figure that out.
It may have something to do with the Site Definition, but I'm just guessing. I've seen this difference in both SharePoint 2007 and 2010.
Right now I'm working in 2007, with lookups to Title columns in other lists. In this case, I don't have the ID;#. It seems to be consistent within installations.
Generally speaking, I would always prefer to see the ID;#, as I can then do much more reliable matching in my AggregateDataSources than if I have to use the text values.