Tony, as Mick said, your questions weren't stupid--they were good ones.
The ticket folder Lois was holding probably was embossed with the name of a real airline. It's usual in films to see corporate logos in passing--for example, someone lights a cigarette, you see a Marlboro box momentarily. But in that scene, the camera freeze=framed and focused on that ticket folder for about 15 seconds while Henry provided a voice-over. I'm guessing that the studio's lawyers advised the production team to black-out the airline's name lest they be sued for infringing on the airline's intellectual property (their logo and corporate name) to show it in a negative way (Lois flies that airline to deliver dope).
This wouldn't have been an issue if the airline were portrayed in a positive or neutral way. In fact, many companies pay movie companies to focus on their logos. Watch people talking on phones in many films of the Eighties and Nineties--the camera will focus on the handset, showing an AT&T logo, even though regular AT&T phones have no logos on their handsets. If you're familiar with "The Shining," watch the scene where Dick Halloran flies from Miami to Denver because he thinks Danny is in trouble--there's a ten-second shot of a Continental Airlines aircraft flying over the majestic Rockies.
In the other scene you mentioned: Jimmy was directing Karen to his stash of swag (stolen goods) and was inviting her to take what she wanted. I don't think Jimmy intended to whack her. As Mick said, her reaction was a product of her paranoia.