For the first 20 years they only carried four digit numbers. Same with the 455s, the Southern ones now carry the full six digit numbers but in the '80s and '90s they had four digit numbers displayed,
The Southern Railway/Region had a long history of four digit numbers for multiple units and the sheer number of SR MUs meant it chose not to change every unit number when TOPS came along.
Thus the original numbering system continued until the 4CEPs were refurbished. They were then renumbered with the TOPS prefix, but in a number series that would not clash with the four digit numbers carried by other SR MUs - hence the numbering of the refurbished units started with 411501, not 411001, because the four-figure version of that would have clashed with the number of 6S Hastings unit 1001.
Early renumbered 4CEPs and BEPs did carry the full six digit TOPS number on the ends for a while. However the Southern was so attached to four digit numbering (plus there was very little room between the end gangway and the side of the vehicle, above the cab windows, which is where unit numbers were displayed, making them hard to read from any distance) that pretty quickly the first two digits were dropped.
The likes of the 455s and 5WES carried the four digit versions of TOPS unit numbers from new. Then BR was privatised and such quirks as the SR's attachments to four digit numbers gradually vanished.
(Interestingly, the 508s always carried full six digit numbers, but this could be because they had a bigger space on the front for the unit number or because they were always regarded as a stopgap)