Well I've found a solution, not very friendly but works, is based on this article
So basically the article says that you need to identify in the query how to include everything that has any value:
Text values consist of alphabetical characters (a..z) and numerical characters (0..9) and use a NOT at the beginning to exclude all the possible values...
The "good new" is SharePoint isn't case sensitive so you have to do it only once per letter, examples:
If you want to filter, let's say by CheckoutUserOWSUSER as in the original question, by an empty value you have to include this in your querytext:
NOT(CheckoutUserOWSUSER:a* OR CheckoutUserOWSUSER:b* OR CheckoutUserOWSUSER:c* OR CheckoutUserOWSUSER:d* OR CheckoutUserOWSUSER:e* OR CheckoutUserOWSUSER:f* OR CheckoutUserOWSUSER:g* OR CheckoutUserOWSUSER:h* OR CheckoutUserOWSUSER:i* OR CheckoutUserOWSUSER:j* OR CheckoutUserOWSUSER:k* OR CheckoutUserOWSUSER:l* OR CheckoutUserOWSUSER:m* OR CheckoutUserOWSUSER:n* OR CheckoutUserOWSUSER:o* OR CheckoutUserOWSUSER:p* OR CheckoutUserOWSUSER:q* OR CheckoutUserOWSUSER:r* OR CheckoutUserOWSUSER:s* OR CheckoutUserOWSUSER:t* OR CheckoutUserOWSUSER:u* OR CheckoutUserOWSUSER:v* OR CheckoutUserOWSUSER:w* OR CheckoutUserOWSUSER:x* OR CheckoutUserOWSUSER:y* OR CheckoutUserOWSUSER:z* OR CheckoutUserOWSUSER:1* OR CheckoutUserOWSUSER:2* OR CheckoutUserOWSUSER:3* OR CheckoutUserOWSUSER:4* OR CheckoutUserOWSUSER:5* OR CheckoutUserOWSUSER:6* OR CheckoutUserOWSUSER:7* OR CheckoutUserOWSUSER:8* OR CheckoutUserOWSUSER:9* OR CheckoutUserOWSUSER:0*)
So now you are sure that you exclude all the possible values for that field and voilá.
Long and no friendly, so if you have another idea please hit it =)