The polymer coated cables are only going to be worth the investment if you have the intention of replacing them as they need it; and not neglecting them until they gunk up and the coating comes off; especially since we're talking brake cables and not shift cables.

"Worth it" subjectively is going to be tough. A set of Swissstop brake pads + polymer cable set for your BR-561's are going to be more in the long run than a 5800 caliper set + couple stainless cables from LBS...considering a pair of 5800 calipers is under $60 from UK, and you can resell your BR-561's for ~$35 on eBay (if they're in good shape). Did this on the other half's bike not too long ago. Biggest difference was lack of flex/'squishy' from the caliper from updated design, which no cable set will fix.