I've read in the law that logos are protected by the United States Trademark law, not laws of copyright. Essentially this means that you have immediate permission to use a logo that doesn't belong to you, without asking for direct permission from the logos owner (as long as you follow legal usage guidelines). So my question is: Do I need to cite these logos I use if they do not have protection by copyright (thereby giving me usage privileges)? And also do assume I would follow correct guidelines and include a standard legal disclaimer.
If you are using simply using the logos in place of the company name, there is no reason to cite them since you would not cite a company name. If you are intending on publishing the work, the publisher may want to see a signed release from the copyright and/or trademark holder.
Logos can be protected by both copyright and trademark. This is entirely orthogonal to the issue of citation. By academic convention, you are required to cite any work which contributed intellectually to your work. If I base my work on a paper from the 1800s, I am still required to cite it, even though it is likely to be long out of copyright. This is not a legal requirement, but a question of academic ethics.
Whether you are required to cite these logos will depend on whether they make an intellectual contribution to your work, and the common practices of the field in which you are working. It does not depend on whether the logos are under copyright or trademark.