Well firstly, it is not the most common fear. Last time I checked, fear of spiders was 9th. (behind: rejection, failure, death, intimacy, dark, heights, public speaking and flying.)
Secondly, you have to take into consideration that only a small percentage of arachnophobics are actually scared to the point where they cant play a game with a spider in it. Most of them are just very uneasy around real spiders.
Removing giant spiders would cater for a very small group of people so it is highly unlikely (nor recommended) that Bethesda would even consider it. Like I mentioned earlier, more people are afraid of heights. Do you want Skyrim to be flat? Didn't think so.
These spiders are not real, if you are severely arachnophobic, wait for someone to mod them out.
I would love to see a version of the game that caters to every single persons phobias and dislikes.
The entire game would just be a blank screen. And there are probably people afraid of that too.