To add the Thameslink core would be confusing as that splits both north of St Pancras and South of Blackfriars. So do they also include London Bridge? Then why not Elephant and Castle, - or might as well go to East Croydon.
Thameslink was on the tube map for years, marked between Kentish Town and Moorgate, Elephant and Castle and London Bridge.
I thought it lasted on there longer, but it looks like it (and the North London Line and Northern City Line to Moorgate) disappeared from the map in 1999.
This map from May 1999 has it: http://www.clarksbury.com/cdl/maps/tube99.jpg
This one from December 1999 doesn't: http://www.clarksbury.com/cdl/maps/tube99-2.jpg
(Maps taken from an archive of some at http://www.clarksbury.com/cdl/maps.html )
Part of the reasoning behind the Thameslink core frequency and train design (fewer seats, more standing, auto opening doors) is given that it's expected to provide relief to the northern line so that would make it seem like it'd be sensible to include it.
Although the December 1999 map was pre-TFL it was probably the last and perhaps the first under TFL-like thinking, as TFL was planned from 1999 and officially formed in 2000, so perhaps that gives weight to the idea that TFL are a little self-obsessed.
I really did think Thameslink was on the tube map more recently than that, but a quick search hasn't found a map with it on. Hmm...
EDIT: I've found one from 2010 and there aren't any National Rail lines on it, so it doesn't look like Thameslink was removed because of the upgrade work, it seems to long pre-date it.