The Tiagra and Ultegra levers I mentioned are both 10 speed. As to whether the Ultegra are left over, not sure. I do not know how Shimano runs its factories. Once Shimano changed to 11 speed on Ultegra, did they immediately stop making all 10 speed levers forever? Or did they make 10 and 11 speed Ultegra levers for years side by side? I'd guess the last. Shimano continued to make the old style for years after shifting to the new style to keep stores and shops supplied with parts to fix older bikes. Its probably not a black and white changeover going from 10 speed to 11 speed levers.
As for upgradability, does anyone make indexed downtube shift levers for 9, 10, 11 speed gear systems? I looked on the Shimano website and saw zero downtube levers of any kind. I see MicroShift does make downtube levers for 9 and 10. http://www.microshift.com.tw/road_Shifters.html
Shimano may overlap series for a short while but they tend to drop production of n-1 rather soon after n is introduced, particularly at the upper level groups. I expect 10-speed Ultegra STIs are not going to be in production long and what you are seeing is a closeout. It's not going to be long before Sora will be the only 10-speed group left in production after it's updated from the current 9-speed (where it's the only 9-speed group now).
Yes, Shimano made 9-speed and 10-speed downtube levers listed as Dura Ace items. The 9-speed ones are probably considered obsolete but the 10-speed versions listed as SL-7900 are still available.
As to Shimano barends, they are still available in 10-speed as SL-BS79. Most of these are sold for Tri/TT bikes for mounting on aero bars but Tourists use them too.
As to Microshift, they provide the 9,10 and 11-speed shiftlevers to Gevenalle who uses them on their brifters. Gevenalle also sells the levers as aftermarket items in all three speeds so, for $70 you could "upgrade" your 9-speed Retroshifts to 11-speed.