clique_number corresponds to the C igraph_clique_number, with worst-case complexity O(3^(|V|/3)). igraph_clique_number iterates over all maximal cliques and finds the biggest size.
The algorithm used for finding all maximal cliques is version-dependent. The docs for the related igraph_maximal_cliques say
The current implementation uses a modified Bron-Kerbosch algorithm to find the maximal cliques, see: David Eppstein, Maarten Löffler, Darren Strash: Listing All Maximal Cliques in Sparse Graphs in Near-Optimal Time. Algorithms and Computation, Lecture Notes in Computer Science Volume 6506, 2010, pp 403-414.
The implementation of this function changed between igraph 0.5 and 0.6 and also between 0.6 and 0.7, so the order of the cliques and the order of vertices within the cliques will almost surely be different between these three versions.