It doesnt matter. The position of the HDD has no bearing on the recording technology. The only position that HDD are not recommended is upside down(This is in the old days and I'm not even sure if this is True on today's drives). Other than that HDD can run. I run my portable drives on different position (upside down, rest on it side, rest on short-side(side w/o the cable).
Majority if not all of the HDD today use perpendicular recording. Again it doesn't matter to your application or need. It will work regardless if you use perpendicular or old recording method.