NestJs: Unable to read env variables in module files but able in service files?

Your .env file is not yet read in when your JwtModule is instantiated. So either read it in earlier e.g. in your main.ts before the nest app is created or better: create a ConfigService and make the dependency on your config explicit:

JwtModule.registerAsync({
    imports: [ConfigModule],
    useFactory: async (configService: ConfigService) => ({
      secret: configService.jwtSecret,
    }),
    inject: [ConfigService],
}),

See this answer on how to create a ConfigService.