If you clean it well in a hot PBW solution and use a properly mixed batch of Star-San you will probably be fine for a while. The acrylic plastic that is used for the auto-siphons tends to develop those micro cracks in hot water. Its not really a problem as I have had my auto-siphon for several years with micro cracks in it and I have not had an infected batch yet :knock on wood:. If it really bothers you, get a new one as they aren't very expensive. I do wish that they were made with a better plastic.
Brewing Soon: Oatmeal Raisin Cookie Amber Ale
Kegged: Scottish Pale Ale (Scottish 80/- with added Hop Tea.
Bottled:Pumpkin Ale & Mcquaker's Chocolate Oatmeal Stout
Drinking: Above & HUB IPA & Dechutes Black Butte Porter