If I ask for classroom accommodations or register with the SSD office will something go on my academic transcript, saying that I received special services?
No, absolutely not. Your confidentiality regarding this matter is assured. Nothing will go on your transcript if you decide to seek out services or accommodations.
Will receiving services or accommodations affect my getting into a graduate or professional school?
No, the services and accommodations you received as an undergraduate are kept confidential. However, you may want to ask those individuals writing letters of recommendation for you NOT to disclose your disability in their letter.