I think where you might run into trouble is when you sell your house in the future. You may have to get a variance for the work after the fact before a buyer will even consider buying your house. More of an issue now than when the market was burning hot.
Saw a LOT of houses where the CO for the basement or even entire second floor were "pending." Some, say it is easier to ask forgiveness than permission.
However, we did see a house that had a wonderful addition over the garage (I think an entire apartment) that was going to ripped out entirely before the sale. Probably didn't comply with zoning and couldn't get a variance. It was an expensive renovation that will cost more to remedy just to sell the house.
I think the reason that a lot of people don't get the permits in the first place is the very real fear that their property taxes will go up substantially. They rather take a one time monetary hit when they have to pay a fine and get the variance later. Also, they may plan to live in the house for a very looooong time where if they have to tear out their work later, they will feel they got their "money's worth" living with the improved space before then.
You should check with your county about the permitting requirements in your area, the potential property tax increases for the improvements, what neighbors typically do and call a realtor about the problems and procedures of selling a house with a finished basement without a permit or updated CO. It might be simple or it might be complicated. Find out in advance if saving $500 will cost you $5000 or vice versa and make an educated decision.
Good luck.