The ICC rankings are purely statistically based and make no allowance for opinions and common consensus. Akram's failure to reach #1 on the rankings is a reflection of the fact that his stats (relatively low wickets per match, high proportion of tail end wickets, relatively few match winning performances etc) do not match his reputation, rather than any flaw in the system. Irrespective of how highly Akram may have been rated by his opponents, journalists and the general public, there was no sustained period of time in which he was statistically the world's best Test bowler.
Having said this, Akram isn't even in the top 75 bowlers ever according to the ICC rankings, which does seem an excessively low ranking, especially when you consider some of the people ahead of him such as Bert Ironmonger, Geoff Lawson and Ken Higgs.
ICC Player Rankings
www.relianceiccrankings.com