As Glenn said, it depends on the heat and conditions you are going to expose it to. If you plan to do a lot of extended dyno work, and or sustained high RPM riding, carbon is not the best material. Its the heat as well as the gasses that degrade the carbon.
That being said, I have over 50k on my TiForce can on my ZRX-1200, including 5 dyno runs on 2 different bikes - and it still looks and sounds like new. TiForce uses stainless steel wool around the baffle, followed by high heat fiberglass packing. It is rare to see a TiForce can that has had the packing blown out from normal street use (ti canisters). So far, we have not had any problems with the carbon canisters either, they seem to be made to the same high standard as the titanium canisters have been.
Many manufacturers will put the carbon skin over an aluminum/titanium/stainless inner skin, to provide extra insulation and protection.
Now - there are some carbon fiber materials that do very well with high heat conditions - but they are usually tremendously expensive.
But basically - yes, the bike shop was good to warn you... If you are a regular street rider, then you can probably go ahead with the carbon can's and never have to worry. If you plan on heavy mods and dyno work and drag racing etc, then I would suggest the titanium canisters.
Give me a shout if you want a good price