Federal law (See 18 U.S.C. 2706) requires law enforcement to reimburse providers like Yahoo! for costs incurred responding to subpoena requests, court orders, or search warrants. Yahoo! generally requests reimbursement when responding to legal process, except that Yahoo! maintains an exception to this policy for cases involving the abduction or exploitation of children.
The law is available here. It's a requirement for law enforcement requesting information, not the organizations providing it (except that the amount is "mutually agreed by the governmental entity and the person or entity providing the information").
A governmental entity obtaining the contents of communications, records, or other information under section 2702, 2703, or 2704 of this title shall pay to the person or entity assembling or providing such information a fee for reimbursement for such costs as are reasonably necessary and which have been directly incurred in searching for, assembling, reproducing, or otherwise providing such information. Such reimbursable costs shall include any costs due to necessary disruption of normal operations of any electronic communication service or remote computing service in which such information may be stored.
So, the guide is a means for law enforcement to interact with Yahoo (and the law) in a standard, easier way. Does it make it more likely that investigators would ask Yahoo for documents if Yahoo makes it easy, as opposed to cooperating as little as possible? Probably. But Yahoo has no reason not to cooperate.