Although the web & thus the content of the web is in the public domain, you must/should abide by the guidelines provided by the website's owner.
If they prohibit deep-linking and advertsie this - you shouldn't.
If however, their TOS or related policies don't mention it, there isn't much of a problem.
You should not however, link out of context, that is... linking only to a deep-linked e.g. applet/image directly without the page (HTML/ASP/PHP etc. This infringes on copyright issues, as the link makes the appearance that such content is yours when in fact it is not.
Also, assuming that you were linking to other sites' homepages (top level page) as well, would this hurt you in SE rankings?
This changes nothing - no negative affects, with the exception that the main page may not be directly related (slightly less relevant) to the topic you were attempting to link to.