Question: Example:
I have a tab "books" with "id" (int autoincrement) as primary key, 
name, author, price etc...(not important). There's 5 books and I delete the book with id=3.
When I add other books the autoincrement value will start from 6 and there's a missed 3 in the id sequence (1 2 4 5 6). So multiple delete/add can create a tab with missing id values if I don't set the autoincrement value or I don't reassign id to books.

Can the situation with missing numbers in id create lowering of performance in queries?

Answer: 
You don't need to worry about performance with missing auto-increment values.

Just make sure you choose the proper [data type](http://dev.mysql.com/doc/refman/5.5/en/numeric-types.html#integer-types) for the auto-increment column so you do not run out of values.
Thats okay with auto-increment. A normal integer field would do the job for a very big amount of data. You could use "unsigned" option to increase this amount.