According to Christian Barth, Esq.:
No it is not legal for to be self-employed if you have a residence permit as a skilled migrant. It violates the conditions of your permit. You can lose your permit and be deported.
You do have the option of filing an application to change your status from skilled migrant to self-employed individual under the new points system for non-EU, non-American entrepreneurs. However, it would be denied because you're not investing enough money or creating enough jobs.
Another immigration attorney, Jeremy Bierbach, LLM, says:
There is a light at the end of the tunnel: after you have been a knowledge migrant for 3 years without interruption (or have had any kind of permit for work for 3 years), you gain your freedom on the labor market (if you renew your permit, it will say 'Arbeid vrij toegestaan. TWV niet vereist.') and then you are free to pursue self-employed activity on the side. Note that it's still a good idea not to quit your day job yet, or at least anytime you have to renew your permit, make sure you have an employment contract that satisfies the requirement of showing you can support yourself (the contract is valid at least one year into the future, and you earn the net monthly norm income for yourself as a single person or you and your dependents if you have any); because proving you can support yourself from self-employment income can be a bit tricky during the first 18 months after you gain your freedom on the labor market.
In theory, you could run a home business up until the legal maximum before reporting the income for tax purposes, but this is not allowed under your permit. You would be skating on thin ice.