You can place your machine horizontal (as opposed to vertical like the case was built) without issue providing the motherboard is at the bottom and not hanging upside side down. I would be more worried about airflow than anything, as long as placing the case on it's side does not impede the airflow, then there should be no problems.
Years ago, all desktop machines were horizontal and we still have some around the office that refuse to die. My HTPC is an newer retro style horizontal case and it's runs 24/7/365 for the past several years with no issues.
Also, it makes no difference whether a CD-ROM is vertical or horizontal, again just so long as it is not upside down.