I use a piece of 9mm for the job, so it doesn't weigh that much extra and doesn't in my eyes cause to much mess for the central maillon. It's the way I was taught and it's the way I've stuck with.
With jammer on rope you only have one cowstail (a short one) - which could make life more awkward in some places(like as you say, pitch heads/traverses). Not so much a problem in caves with a horizontal/vertical mix but in some pots it would be a faff to keep clipping/unclipping the jammer.
There would appear to be a small possibility of dropping the jammer - ie. it's not attatched to anything unless you have the cowstail attatched - obviously attatching the tail before unclipping jammer from harness would help matters, but the potential is there.. Lets say you were mid descent and have a problem, you need to change over - unless you clipped the cowstail to jammer at the pitch head after you had finished with them on traverse etc then you have to do it mid pitch, which is probably where the greatest potential for losing it exists - more so I would have thought if it was a small/tight pitch with not much room for movement.
Not often used in descent but, at a hanging rebelay - you hang from short cowstail with long cowstail on rope you just came down with descender reattatched you need to take weight of short tail.. It might not happen often but you need to use jammer to get weight off short cowstail - thus you need to remove your backup cowstail to use it.. Which means your only backup is then a jammer which if you had made an error in threading the descender (ok, this is rare but the potential does exist for it to happen) then your backup is the jammer which is not recommended for a shock loading.