Why are ports on top? Because it's a design holdover from full towers that used to sit either on the floor or in a cubby next to the floor. Added with multiple optical bays, floppy bays etc that ate up higher access (the bottom being all fan space, that left the top as the most viable spot. It's also more practical in the sense that a USB plug sticking out the front of a case is definitely in a bad spot when ppl or animals go past, they get broke off quick.
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There's been all kinds of pc's built in open air, even the ones designed to hang on the wall like a picture, just a little glass in front to protect from direct contact. They have one thing in common. The owners spend more time cleaning out the dust than they do gaming or using the pc. A case does a lot more than be a box designed to hold the components, it's also for protection of the components from outside abuse (like when the cat jumps up on the desk, or your 3 yr old discovers she can throw dolls) and they also protect the components from excessive, immediate dust. Pull the side panel off if you want to, just invest in multiple cans of compressed air, your cleaning regimen will go from every few months to every couple of days.