There are two meanings here: 1. You might be building your GIS as Shadow IT, know the pitfalls and realities. 2. Beware your GIS 'clients' may be building Shadow GIS underneath you. 

Shadow IT is a real thing. It's talked about at conferences and even has a Wikipedia page. Essentially, it is when 'unofficial' tech infrastructure is built in parallel to the official IT department; sometimes sanctioned, sometimes not. GIS could exist as a Shadow IT in both positive and negative way