https://www.investopedia.com/f... this is a good read for you. Regarding the question to pull a permit or not, usually you would go with: if it's visible from the street you most definitely want a permit (windows, roofing, having a dumpster). If it's an extensive rehab: new electrical, re-plumbing, etc. even if not visible from outside, I would pull a permit. It also matters what you plan on doing with the house. If you flip it, the buyers will likely want to know if you had permit. If you plan on keeping it for long term, like rental, you might get away with it but insurance might ask you for records.
You also need to be careful on the order of the work. If say you do plumbing and windows the same time and the inspector comes for the windows, they might notice the other work and ask if you have permit for that and get you in trouble. So plan accordingly.
Lastly, if you did have the contractor pull a permit, make sure to check with the City Building Inspections the status of your permit after they are done. Many times contractors will "forget" to call a final inspection. In this case your Status will show something like: Inactive, instead of Closed or Approved... or put it in the contract you want them to call final inspection as you will not consider the work done until that happened.
As for "Opening the box of worms", I think it is beneficial for you to have an inspector and validate the work done. For the contractors is not, as they are going to be delayed, need to wait for the inspector and if the inspector finds something wrong, they need to fix it and they most definitely can not cut corners. Usually the inspector will know more about how things should be compared to you, so this would benefit you in the end.
I had for example occasions where the electrician said they are done and I thought it's good, but then the inspector came and turned out that some wires were not proper and they had to fix it. Had I not pulled permit, I would have been left with the bad wiring and not even know about it. Would have been an issue from it? Maybe not. But I am happy I had it fixed.