The plural of wiki is wiki, not wikis. In the singular we ambiguously say a wiki, short for an install of wiki.
The grammatical distinction is between count and noncount nouns.
When used as a noun, wiki refers to a mass of pages, or when federated, a mass of sites. In context wiki can refer to a single install but this usages doesn't generalize.
In the abstract sense: "seek the wisdom of wiki"
In the count sense: "update wiki before you go"
When used as an adjective, wiki describes a style of collaboration. A wiki site. The wiki way.
The wiki encyclopedia, Wikipedia, is an encyclopedia where editors collaborate the wiki way.
When we say a wiki, we are using wiki as a noun, as a shortening of an install of wiki, just as one might say a coffee as short for a cup of coffee.
A wiki as short for an install of wiki becomes ambiguous under federation where we are as likely to be referring to a page of wiki or a neighborhood of wiki.
Similarly hypertext has become a mass noun that could equally refer to a document of hypertext or a world wide web of hypertext.
Discussion
But you can have two coffees, as in two cups of coffee. That’s what “two wikis” means, isn’t it? twitter 
That usage presumes a wiki is a site just as two coffees assumes a coffee is a cup. This breaks down under federation.