1) "am I freeloading, or am I a (financially) valued customer?"
Depends. Most bike shops I've been to are happy with giving some of advice -- helping the person find the right part and them do it themselves, since thats how a lot of bike upkeep is done. Of course, doing this too much can annoy people and also choice of timing -- if the shop is just sitting idle, theres probably less annoyance than otherwise. Also, the level of detail -- if you have to be walked through a lot of the repair and it takes a lot of time, that can also be annoying (though some shops are happy to do this and rent tools so people can do this, like an Autozone shop or similar). Most people should be able to judge their behavior on their own.
If you want to get advice and stuff as a primary thing you do at a bike shop, you might want to join a bike co-op if you have one in the area. Most are friendly towards people learning from each other how to do things in a shared space and a lot of them have (some) parts available for sale for the community, and you can pick up remaining parts at your LBS.
2) "putting disk brakes on a 90's Hardrock frame, they will suggest that it will be easier to just get a new bike"
Yeah, because it is the sensible choice. You'd need new brakes, but also new wheels so the rotors mount, and a new fork to have the brake caliper mount. The rear may be handled with an adaptor to mount the caliper. This would probably cost about as much as a basic hardtail with disc brakes on it now. I'd be worried if anyone suggested that it was a good idea to proceed with adding disc brakes to a 90s Hardrock frame.
3) "what are the typical profit margins on new bikes, repairs, and parts?"
Depends a lot on the type of shop, where you are, brands they carry, how much they charge for repairs and parts. Some mom and pop bike shops are now using amazon as (part) of their part suppliers, which sets pricing one way; others use big suppliers like Quality Bicycle Products (QBP), though you can't see the pricing for the QBP catalog directly. Comparing prices of parts you bought to online is one way to get an idea, though that doesn't properly weigh overhead between the LBS and online.
The profit margins on repairs depends on the repair; if parts are broken out separately (as they are in many places) from the labor, it's the technician's time vs cost. Some places do x dollars/hour of labor, and charge you that way. Other places charge you for the type of repair at a flat fee, which may be set based on time it takes on average or just to have reasonable profits.
The way I see it, don't worry about it too much unless you feel like you're being ripped off (in which case go shop somewhere else); after you live in an area for a while, you get an idea of which shops are good/bad. LBS's have more overhead than online places since they have to pay for buildings, staff salaries, etc.