Hi all, Interesting, I didn't know that, but I've never kept Guinea Pigs.
I don't think it will matter as long as you don't over do it. Rodents and Lagomorphs are very efficient at retrieving the nutrients from their food, they have an enlarged caecum and eat their own soft faeces, so the hard pellets are largely indigestible structural carbohydrates (lignins etc) having had 2 passes through the digestive system.
If the pellets contain some urea it may actually be an advantage. Because they are in the substrate any ammonia resulting from the microbial decomposition of urea:
(NH2)2CO + H2O → CO2 + 2NH3) should be scavenged pretty efficiently by your plant roots.
cheers Darrel