Now that we have direct, explicit confirmation that submarines are being worked on ( yay ), here 's a side project I’ve had: documenting all the ships currently in the game, and CDK, which have depth charges modelled on them which are unused.
This list does not include ships which also have loadouts for depth charges which are unused, whether or not that overlaps w/ them having the weapons modelled. For a list of those unused loadouts, use @gszabi99 's Naval loadouts list.

Depth charge rails on USS Cleveland. It 's currently the highest BR vessel to have some.
Ships which have unused depth charge rails:
FRA: Aigle, Milan, La Combattante(destroyer), Chacal, Leopard, Panthere, Le Triomphant, Vauquelin, Aconit, Marne, Aisne, Le Brestois
DE: Z12, Z15, Z43, Z46, Z47, Z4 Zestorer, Karl Marx, Drache
ITA: Albatros F543, Alcione F544, Attilio Regolo, Comandante Margottini, Geniere D555, Impetuoso, Leone, Grecale, Da Verazzano, Aviere, Corazziere, Geniere, MAS 441, MC-485
JPN: Agano, Furutaka, Kako, Sendai, Yubari, Akizuki, Ayanami, Hatsuharu, Hatsuzuki, Hayanami, JDS Isuzu, Kiyoshimo, Matsu, JDS Murasame, Nenohi, Yugumo, JDS Yugure, Yukikaze, Tsugaru
GB: HMS Enterprise, HMS Hawkins, HMS Churchill, HMS Montgomery, HMS Grafton, HMCS Haida, HMS Calpe, HMS Brissenden, HMS Jervis, HMS Kelvin, HMS Nepal, HMS Eskimo, HMS Mohawk, HMS Vega, HMS Verdun, HMS Abdiel, HMS Saumarez
USA: USS Atlanta, USS Cleveland, USS Barker, USS Litchfield, USS Welborn C. Wood, USS Aylwin, USS Fletcher, USS Bennion, USS Cowell, USS Gearing, USS Frank Knox, USS Mitscher, USS Wilkinson, USS Porter, USS Moffett, USS Phelps, USS Somers, USS Davis, USS Sumner, USS Coolbaugh
USSR: Besposhchadny, Ryany, Soobrazitelny, Stroyny, Moskva, Tashkent, Ognevoy, Letuchiy, Pr.201K, Pr.201M, Yenot, Rosomacha, MPK-33

The Squid mortar, seen here on HMS Armada. I started this project when I found this, and then kept finding unused things similar to it.
Ships which have unused depth charge mortars:
FRA: Leopard
ITA: Impetuoso
JPN: JDS Ayanami
GB: HMS Armada, HMS Tobruk, HMS Daring, HMS Diamond, HMS Diana, HMS Leopard
USA: USS Davis, USS Coolbaugh, USS Dealey
USSR: Admiral Kuznetsov, Baku
Depth charge storage in Syonan. One of the largest by number of DP present.
Ships which have unused ammo storages for depth charge rails:
FRA: La Combattante(destroyer), Panthere, Chacal, Leopard, Vauquelin
ITA: Impetuoso
JPN: Syonan, Type 4 (Mod. 2), Type 4 (Mod. 4), Ha-go (Mod. 1), Shisaka
GB: HMS Hawkins, HMS Garland, HMS Grafton, HMS Calpe, HMS Brissenden
USSR: BMO, MO-4

Reloads for mortars on Vautour. Only the charges loaded on the mortars are available ingame at the time of writing.
Ships which have unused ammo storages for depth charge mortars:
FRA: Vautour, Leopard, Panthere
JPN: JDS Ayanami, Ikazuchi, Type K-8 No.13(early), Type K-8 No.13(late)
GB: HMS Churchill, HMS Montgomery
USA: USS Cowell
USSR: Spokoniyy, Blagorodnyy, Pr.122bis, Admiral Kuznetsov, Baku

Additional depth charges on USS Fletcher, visible, yet unusable.
Ships which have reloads for depth charge rails on their visual model, but not in the X-ray:
FRA: Aconit
JPN: JDS Yugure
GB: HMCS Brantford, HMS Liscomb
USA: USS Fletcher, USS Bennion, USS Cowell, USS Sumner
USSR: SKR Groza, Spokoinyy
Unusable reloads for the mortars of Aconit.
Ships which have reloads for depth charge mortars on their visual model, but not in the X-ray:
FRA: Aconit
JPN: JDS Yugure
GB: HMCS Brantford
USA: USS Bennion, USS Phelps, USS Davis