I'm creating a Joomla Component that will allow site visitors to download a seem file (whether it is mp3, or wave, is not important). Individuals files are handled within the admin interface and may be unregistered inside.

Therefore, it appears that placing them within the assets section isn't a choice, because it will make them accessible from the server. I wish to avoid immediate access and just serve them through my MVC structure (usnig RAW document type) after verifying the asked for file is released.

What are the conventions around the positioning of individuals files within my component's directory structure?

My first idea is to produce a folder within the administrator/components/com_mycomponent and the files there. Should i restrict use of this new folder with a brand new .htaccess file, or perhaps is it already taken proper care of by Joomla having a global .htaccess?

you need to put the files in media directory. It's based on the installer and is way better place. The logic would be to have code in com_mycomponent for site and admin and each of individuals will share media (images/css/js), downloads, etc...

/media/com_mycomponent/

Limitations are your decision.

Here's Joomla installation structure, http://docs.joomla.org/Components:xml_installfile