How specific of references can I make in a book without breaking the rules?

The only thing you might have a problem with is mentioning the name of a real shop "a local coffee house called the Depot that really does exist" so that coffee shop owner may take exception to you mentioning their name in the novel. Although you say how good their coffee really tastes, the proprietor may not want their shop mentioned if the rest of the book is about something detrimental or vulgar or obscene or about some awful incident that may reflect badly on their business even despite the glorious outpourings of admirations. You could go talk with the owner and ask permission and if they refuse, you will need to change the name of the shop in the novel. It just might be safer to call the shop "The Depotter" or some other sort of name mixture that might infer it to be The Depot but could actually be a made up name of a fictitious business.