Note: This post is only covering the naming conventions of the major combatant vessels of the Imperial Japanese Navy.
Aircraft Carriers
Named after birds, dragons, and mythical flying creatures
Example: Shokaku (翔鶴)
Meaning: “Soaring Crane”

Battleships
Named after old poetic names for Japan or old names of Japanese provinces
*Even though the Kongo-class were upgraded to battleships later in their careers, they retained their names in-line with originally being battlecruisers.
Example: Yamato (大和)
Meaning: Literally “Great Harmony,” but Yamato is both an old Japanese province and an ancient Japanese name for Japan itself.

Heavy Cruisers & Battlecruisers
Named after mountains
*The Mogami-class cruisers were originally laid down as light cruisers, so they received the names of rivers.
Example: Takao (高雄)
Meaning: Named after Mt. Takao outside of Kyoto. Not to be confused with Mt. Takao near Tokyo or Mt. Takao in Taiwan (Formosa).

Light Cruisers
Named after rivers & streams
Example: Kitakami (北上)
Meaning: Named after the Kitakami River in Iwate Prefecture, Japan.

Destroyers
First-class destroyers
Named after meteorological phenomenon in poetic style
Example: Shimakaze (島風)
Meaning: “Island Wind”

Second-class destroyers
Named after plants/trees
Example: Momo-class destoyer, “Hinoki” (檜)
Meaning: “Japanese cypress”

Submarines
Given a number sequence
Example: I-400 class submarine, I-401 (イ401)

Smaller Warships/Coastal Defense Vessels
Named after islands
Example: Shimushu (占守)
Meaning: Named after Shimushu (AKA Shumshu) island in the Kurile Islands.

Torpedo Boats
Named after birds
Example: Chidori (千鳥)
Meaning: “Plover”

Other Notes
No Japanese naval ships were named after people.
While western navies use prefixes, such as USS (United States Ship) or HMS (His/Her Majesty’s Ship), there is no similar prefix usage in the Imperial Japanese Navy for their vessels. Some works may prefix IJN (Imperial Japanese Navy) or HIJMS (His Imperial Japanese Majesty’s Ship) to Japanese naval vessels, but this is purely a western convention (Chen, 2007).
Furthermore, while many Japanese ships were given poetic or traditional names, it’s unlikely that a Japanese person would interpret those names in a literal sense any more than an American would interpret the literal meaning of a U.S. Navy ship’s name (Chen, 2007).
References
Chen, C.P. (2007, Sept.). Naming Convention of Japanese Navy Ships. Retrieved from https://ww2db.com/other.php?other_id=26.
Hara, T. (1967). Japanese Destroyer Captain: Pearl Harbor, Guadalcanal, Midway – The Great Naval Battles as Seen Through Japanese Eyes (F. Saito & R. Pineau, Trans.). Annapolis, MD: Naval Institute Press.