The way drains were designed a long time ago often won't meet current codes. So, if you start replacing bits, you have to bring them up to code. If you find that the CI in the bathroom is shot and needs to be replaced, you probably couldn't just replace exactly as it is now. Without seeing it, you won't know. It was not uncommon to use S-traps on sinks and minimize the vents. So some or all of the room may not be vented, either. So, the layout may have to change to meet current codes when replacing.
It can get complicated.
As to costing more for a permit, first, you have to pay for it, the plumber has to fill out the application, then wait around for maybe a rough-in inspection where he can't continue to do work and is at the mercy of the inspector arriving, then again at the end. All this adds time into the project, and time is money. In theory, anyways, it should meet code when done if inspected. There are lots of ways that will work most of the time, but don't meet code. Some of these shortcuts may be made if it isn't going to be permitted and inspected if it can make the job faster and easier. Depends on the plumber, his pride, and local codes.