Yes, Fish and Ships works with this 3rd party multicurrency plugins:
- The official WooCommerce multi-currency plugin: link
- The WPML+WCML MultiCurrency plugin: link
- Aelia, premium multi-currency plugin: link
- WOOCS, freemium multi-currency plugin: link
- Multi Currency for WC, freemium plugin: link
- Support for WP Wham Currency Switcher, freemium plugin: link
Custom shipping rates for different currencies (as option) is supported for WPML+WCML, the official WooCommerce multi-currency plugin, Aelia and WP Wham CS.