It has been investigated, it simply has not been prosecuted.
The investigation started when someone reported suspicious activity in Hastert's accounts. The investigation proceeded from a belief that he was being blackmailed. After listening to a wire of a conversation between Hastert and the alleged blackmailer, the officers investigating decided it was not a simple case of him being blackmailed--they or the prosecutors' office used their discretion to go after Hastert for illegally structuring his payments to avoid anti-money-laundering reporting laws, and to my knowledge have not yet pursued any blackmail charge.
Police and Prosecutors have very wide discretion regarding what charges they bring.
In addition, it is very common to have a civil lawsuit brought that implicates criminal laws, but not have the criminal violations be charged. For example, if you steal a purse you go to jail, but if you steal a building you are rarely charged with a criminal offense. It is rarely to a civil litigant's advantage to bring up criminal matters and there are ethical rules limiting the interaction between the two.