I don't technically have any GM authority in this RP, but I am familiar with Kads systems, so here goes.
Human troops are a free for all regardless of races chosen and i assume shaded would apply to them, nightmares and skaven are both natural fits for 'working in the shadows' so I imagine it would apply to the two of them as well.
It also occurs to me I may have misinterpreted, In the past Kad has asked that players add a cost to standard units when adding an ability such as that, usually from an added 50% to 200% base cost depending on the scope and power of the ability in question. Theoretically he should have already mentioned that if it were the case, otherwise I would just assume the 'downside' of the shaded trait means it just applys to all your troops at no additional cost.
... Course I also know what assumption is....