Historically, if a ship carrying gold sinks, whoever salvages the gold/loot gets ownership of it. However, if the ship is a warship, the loot belongs - FOREVER - as the property of the nation-state (or their descendants). This has led to some legal battles over nautical salvage in the Atlantic (were those "Spanish Galleons" military or non-military? Hundreds of millions of dollars depends on that answer during some lawsuits in the 1990s) or nautical salvage in South East Asia where artifacts from long gone kingdoms (that didn't reflect borders created centuries after they collapsed) end up in court over what country gets to show them in museums.

So yes, if you need to move national quantities of gold/silver across the ocean, then for legal reasons, it is best to ship it via your navy.