Retaliation protection still applies
No. In California it is illegal for a landlord to retaliate against you for reporting unsafe conditions or code violations, and that protection applies even when the unit itself is unpermitted.
Civil Code Section 1942.5 protects tenants who exercise their rights, such as complaining about habitability problems or contacting a code inspector. If a landlord raises your rent, cuts services, or tries to evict you shortly after you reported problems with an illegal unit, the law may treat that as retaliation. In certain situations there is even a legal presumption that punishment following soon after a protected complaint was retaliatory.
Landlords sometimes try to use a unit's illegal status to scare tenants into staying quiet. But you do not lose your protection against retaliation because your unit was unpermitted — the landlord is the one who rented an unlawful unit.
Keep records of your complaints and the dates of any landlord actions that followed. If you believe you are facing retaliation for raising concerns about an illegal unit, a free, confidential review can explain your rights and options.
This is general information about California tenant rights, not legal advice. Every situation is different.