The article mentions high temperatures and acidic conditions, so your cables will be safe. Polyurethanes are not very resistant to acids and will also oxidize over time, especially at higher temperatures. The bacteria are probably making use of this process and speeding it up with enzymes. Clear PU (such as tubing) tends to yellow noticeably over time as a result of the oxidation, and certain types of PU are also known to disintegrate after a few years, though we generally use the stuff that doesn't.
Article doesn't say what type of PU we're dealing with either. It's a broad church. There's cast PU resins, foam, and thermoplastics - both rigid and elastomeric. The commonest are made from esters, though ether and ketone variants are also available for more demanding applications, albeit at a higher cost. As a copolymer there's also a wide variation in the number "hard" and "soft" segments that are strung together. The bacteria will probably favour one or the other, so I'd expect only certain PUs to be significantly affected.
There's also no isocyanates in the finished material, though thermal decomposition releases all sorts of stuff - as does burning wood to be fair. Chemically, the simplest PUs are very similar to nylon, and it was actually developed by Otto Bayer in the later 1930s as a direct response to the tight patents Du Pont had on their nylons.
As far as recycling goes, thermoplastic PUs (as used on cable sleeving) is compatible with PVC, so when that stuff gets reprocessed there is often some amount of PU mixed in the recycled PVC. The companies that recycle cables are only after the copper, and a lot of the sleeving goes to waste. It sells for less than $100/tonne and they generate spoil heaps of the stuff. Need something that eats PVC. It lasts much longer and we use a heck of a lot more of it.