There is some thoughts as to if the feature from SH3 can be ported over to SH4...long shot but would be DAM SWEET!
http://www.subsim.com/radioroom/showthread.php?t=115324
The only way now is to do it on your own, using for example Photoshop or an equivalent image software. Find your "Insignia" and place it on to the skin directly.
Or ask if some of the guys would like to do a custom one for you if you provide the "Insignia" graphics...of course