According to this link, it says that JSON Custom Search API provides 100 search queries per day for free. If you need more, you may sign up for billing in the API Console. Additional requests cost $5 per 1000 queries, up to 10k queries per day.
I have been using the JSON Customsearch API which is https://www.googleapis.com/customsearch/v1
for quite a while now. Yesterday, I fired around 360 requests. So does it mean that since I crossed 100 search queries, I'll be charged for it?
The reason that I asked this was because my Dashboard doesn't show any charges yet.
Yes, you need to pay it. According to my experience, the charge information on Dashboard do not refresh all the time.