No, a stolen car does not entitle you to a refund and the e-vignette remains valid until the end of the purchased time period.
In this case we recommend trying to claim a refund of the e-vignette via your car insurance company.
If only your license plates have been stolen, you can request a change of the registered plates in the web portal under "Requests, Suggestions and Claims, providing the authority with the police report, e-vignette payment receipt, and both vehicle registration documents (old and new, incl. VIN).
Related articles:
Can I get a refund if I buy the wrong Slovak e-vignette?
Do I receive a refund, if I take my vehicle off the Slovak roads and return the number plates?
Can I transfer my Slovak e-vignette to another car?
Can I change the license plate on a Slovak e-vignette?
Slovak National Motorway Company (NDS) contact information (Slovak authority)