Are the prices on car rental price comparison sites (eg: Kayak, Expedia, etc) what you will really end up paying? Or are there a bunch of hidden "extras"?
No, in nearly every case, you will pay more than the Kayak etc sticker price. But this is not because you have to, but because the price excludes most of the extras that any reasonable person hiring a car is likely to choose - the key one being complete insurance, but as Mark Mayo mentioned there are others.
I'd like to know how to more accurately plan out such expenses when planning future vacations
The surefire approach to this is to check the rental company and attempt to book the same car through them directly. Make sure you select all the extras you need, and the price before checkout will be an accurate reflection of what you will spend.
Another good thing to do though, is check if any of your credit cards offer eg. loss damage waiver cover or other extra car rental insurance when paying with that card (this is a typical feature of platinum cards). If so, then you just need to cultivate a clear understanding of what insurance is included in the 'no-frills' product offered by Kayak et al, and whether your credit card insurance closes the gap sufficiently for your comfort/risk appetite. Then you can keep on booking with the convenience of Kayak, but know you have the cover you need.
Just make sure you read the fine-print on the credit card provided insurance, because as this Wiki article details, there are often many exceptions or limitations.