Given that many authors now follow the hybrid Reeses Approach, it is a good idea to include a clause in any agreement signed that explicitly states that those books which the author directly e-publishes on their own instead of traditionally publishing through the agent and a publisher who will produce physical copies are exempt. But any ebook royalties on the electronic sales of those books published through traditional publishers and negotiated with the help of the agent are included in the commissions they would expect to receive.
The agreement should be short, simple, and clear. I am not a lawyer, but that is my opinion.
So yes, I am a believer in the Reeses Approach to book publishing. I did sign with an agent and I am anxious to sign that first deal with a traditional publisher that he is working to line up for me because I see value in getting hard copies into bookstores and gaining access to the international markets that would be difficult to penetrate as an indie-only writer. I am also loving the indie publishing route and am looking forward to completing the new trilogy, getting those books online, and participating in all of the exciting marketing opportunities for indie writers.