For companies like Atari they still have the rights to the games and artwork. However, it seems they don't care for a small market like the arcade collectors' when repro's get made.
Even Nintendo, who is normally extremely strict actually knows about it and more or less communicated they didn't care (in the US). (Source, KLOV forum)
A lot of other companies have long gone, and even if the rights were transferred to other companies they don't seem to mind.
Gottlieb is an exception. They do not want scanned manuals etc. to be available for download and f.i. Phoenixarcade has a license to sell their repro Gottlieb artwork.