Can I install and develop a store (magento) at mysite.com/store - and then later, after its done, apply/assign my SSL cert to mysite.com ? (which I would then assign only to store pages). Or do I HAVE to assign the SSL cert first.

Your SSL certificate should get assigned to your domain (mysite.com) and then you're free to use it in any section or page of your site. So you could use it with mysite.com/store or mysite.com/blog or mysite.com/index.php

It's a domain level thing and not specific to any pages or sections of the site.

Yes you can create your store first and add the cert later on - I do this all the time because there's no point buying the certificate until you really have to.

Most shopping carts have a setting where you can turn SSL on or off, normally I just leave it off while the site is being built which allows for testing checkout/secure pages without SSL. When it comes to the time get the cert installed and retest the cart - job done!