The seeds of gymnosperms are considered 'naked' as:
Their seeds remain exposed on cone scales.
The word gymnosperm comes from Greek words meaning naked seed. In these plants, such as pine and deodar, the ovules are not enclosed in an ovary, so the seeds that develop from them are not covered.
The ovules are borne on the surface of scales of the female cones. After fertilisation they develop into seeds that remain lying on these cone scales, exposed, which is why the seeds are called naked.
Seeds that develop inside fruits are the feature of angiosperms (flowering plants), where the ovary ripens into a fruit that covers the seeds. Gymnosperms have no ovary and no flowers, so they form no fruits, fleshy or otherwise.
Gymnosperms are mostly wind-pollinated, with pollen carried from the male cones to the ovules by air, not by insects. So the seeds are called naked because they lie exposed on the cone scales.
Hence, Their seeds remain exposed on cone scales.
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