Self-Employed work experience is work experience, so it should and must be counted.
If your work experience is genuine and you have supporting documents there is no need to worry.
Again lot of things depend on your NOC.
For eg. Some architects may work freelance or some may run a company(self-employed), many doctors will have their own practice, but a freelance/self employed nurse maybe unheard of.
Secondly with freelance work it maybe difficult to prove the number of hours you spend per week on a job.
In case of self employed work you may need much more documents to prove the type of work you do, eg purchase order from clients, client's contact details etc.
In short lot of documentation...