Indexing is important, useful and yes, has some impact on server performance. However, indexing is crucial across all areas of the product as it allows us to “consolidate” information so we don’t have to cycle through every message and all the headers in an user’s inbox when they, for example, perform a search. Take a customer using EAS on a mobile device. This is a server query, not a local query. Without the index, we have to go through all messages, which would destroy the performance of the mail server PLUS take forever for that user to see a result. That said, indexing is tuned for extremely large servers, which enables us to accommodate many domains and many users on a single box.
As an aside, here's a great Community post on improving disk i/o for SmarterMail that others may find useful: http://portal.smartertools.com/Main/frmThread.aspx?threadid=87919