The 2009 online version of the sectional appendix (on
NR» 's website) explains (at the time of its publication) that
HSTs▸ were not cleared on the SW main line between Basingstoke and Clapham Jn. They
are now cleared between Basingstoke and Byfleet Jn, where they head off to Virginia Water, thereby joining the Reading - Waterloo line which they are already cleared for. However, even this route is shown as fairly restricted in the 2009 SA, with speed limits of 20 mph or less through a number of stations, (indeed Bracknell is 5 mph up and down although not relevant to the route being discussed here).
Not cleared doesn't necessarily mean they can't physically run up to Waterloo directly, just that they haven't yet checked that route out. (Only a subtle point though.) Apparently current policy is that they only undertake route clearance for a class when they definitely need to, ie just in time. After all it is highly likely that the Mk3 HST coaching stock would be OK, because the Mk3 442 is known to be OK (although as it happens, 442s were not allowed into all platforms at Waterloo either)...
However, there are also platforming restrictions at Waterloo, HSTs are only cleared for 17, 18 and 19, for which access is normally only from the Windsor side approach from Clapham Jn, so there'd be very little point in going through vehicle change procedures for the main lines yet.
Link added:
http://www.networkrail.co.uk/browse%20documents/baseline%20capability/gauge%20capability,%20route%20availability/wessex%20route/table%20d3_gauge%20capability_coaching%20stock_wessex%20route.pdfPaul