Currently out of stock of TB900 / TB996 / TB999 and TB1198 belts - hopefully back in stock in 2 to 3 weeks https://www.ducatiforum.co.uk/threads/exact-fit-timing-belts-forum-subscriber-discount.38123/
There is evidently some cross over on 2002 748E models so not necessarily the case. 5 bolt side covers are TBST4 belts. All older models with 4 bolt are TB996 belts... apart from 748R which use TB748R belts.
Yes, 5 bolt models were the last to be produced - I bought one in 2002, just fitted belts a couple of weeks ago and as far as I am aware they were designated as E models as opposed to Biposto although I have seen older models referred to as being E. As you say, surefire way is to check the rocker pin covers for number of securing bolts.
It might have been Nelly who mentioned 2002 E models used both types of head - clearing the shelves perhaps!
Look at the pictures Exige has put up earlier and count the fixing bolts on the plate between the cams.
I thought the crossover from T95 to T93 was early MY01. The S models in both MY01 and 02 share the same engine as the E and are usually 93T