how long do these letters usually take?

As long as the store likes up to the statute of limitations. Often several weeks up to a couple months.

What do they do with my personal info?

Generally they use it to identify you in the context of banning you from their store and suing you if you fail to perform on the civil demand.

Can I do anything to get my info out of their systems?

No.

Are they likely to file charges?

That's not a question that can be answered here. Certainly some stores do file a compliant the police that results in charges being brought. Some don't. It's perhaps more likely that they will pursue the issue than not. Stores can't afford for people to know they don't pursue shoplifting.

if I do get the civil demand and pay, is there any way to ensure they can't pursue legal action?

Not really. But in the unlikely event that occurs, your lawyer is likely to get some mileage with it. It seems likely they could get back whatever you paid for the civil demand.