How Closely Did Afrika Korps simulate the actual campaign conditions?
Not very well at all, but good enough for a board game.

The impact of Malta is reflected in-game as the difficulty of the Germans getting reinforcements and resupply as the game goes on. (I'd get the rules out and cite a detail if only my brother didn't end up with the game; I got Waterloo and D Day, he got Afrika Korps and Panzer Blitz; the local games club got the rest when we moved out).    

Of particular interest is that the air element of the campaign is utterly missing.  

Balance with "historical" verisimilitude is a very tricky thing.  Afrika Korps is not one of the more complex AH games (I played them all from about 1970 - mid 1980's).  A wide variety of decisions made outside of that theater left both Rommel and Monty with constraints on their resources, and how to make that work "in game" can be tricky.  The 'trickle in' gamism of reinforcing units is reasonably close to how things played out. The relative ineffectiveness of most Italian Divisions is also "close enough" to work in the game.  

I've seen games of Afrika Korps won using zones of control and a Recce Company choaking off supply trains at the left edge of the map when Rommel is near to El Alamein.  :-)   IRL, that's not gonna work.  

I did not study that campaign in detail until after college, and played it mostly in high school and college.  With the game as an introduction, it was nice to be familiar with the topic, but as one reads the history one begins to see how a game has to take a lot of short cuts with verisimilitude to arrive at a playable state.  (Midway was kind of clunky).  

Something you may want to appreciate is that the sales brochures that AH put out back in the 60's and 70's had a "complexity" assessment for each game.  Afrika Korps was one of the easier games; 1914 was a nightmare of complexity.