Yes your application will proceed further and of course you will get to sit in the exam. The revised exam pattern of CUET mentions that candidate have to choose a maximum of 6 subjects out of the given 27 domain subjects and you've chosen 3 then it is totally fine.

Moreover you must check out the requirements of your preferred university when you select your domain subjects.

Read more about CUET exam here : https://www.careers360.com/exams/cuet

Anyways, All the Best for exam !!