Why were Japanese submarines not able to defend in the Battle of the Philippine Sea?

By 1944, US submarines were very experienced and had ironed out their problems with their equipment. They had been conducting an extremely successful offensive campaign against Japanese shipping since the beginning of 1942, and unlike German U-boats, had not taken heavy losses and so gained in experience. They had fixed the flaws in the Mark 14 torpedo finally giving them a reliable weapon.

In contrast, by 1944 the operations of Japanese submarines were severely limited by both fuel and Allied air superiority. The Allied experience in fighting the Battle Of The Atlantic; convoys, radar, sonar, air support, plus a huge production of US destroyers to protect convoys; was put to use in the Pacific. This meant little easy pickings for the Japanese submarines. Japanese submarines were often pressed into service to resupply Japanese garrisons behind enemy lines. All this meant they did not have the operational experience that the US had.

Strategically, the US knew the Japanese were coming and from what general direction. The night before the battle they'd intercepted a radio transmission. Radio direction finding gave the position, and the content let them know it was the Japanese carriers. The US could position their line of submarines so the Japanese fleet ran right over them.

In contrast, the Japanese were surprised by the US attack on the Marianas. They were looking to engage the main US fleet and so attacked. In doing so they could not put out a picket line of submarines for the US fleet to run over.

Tactically, that US submarines were attacking during a pitched air battle gave them a great advantage. With ships maneuvering at high speed and watching for aircraft they'd be less likely to be spotted in the chaos.

Once the battle was joined, the major advantage the US submarines had was poor Japanese damage control. Time and again, relatively minor damage to Japanese carriers is magnified by out of control fire and failing damage control systems.

Albacore only hit Taihō with a single torpedo...

However, the sixth torpedo struck the carrier on her starboard side, rupturing two aviation-fuel tanks.

This might seem bad, but putting fuel and water tanks on the outer hull is a form of anti-torpedo defense. The liquid fuel will dissipate the shock and slow fragments. Taihō was able to quickly repair the worst of the damage.

Putting fuel tanks in the path of a torpedo might seem like madness, but liquid fuel will only burn as a vapor mixed with oxygen. A full tank (or one filled with an inert gas) will not burn (sorry, Hollywood). But that vapor became a problem...

Initially, the damage to Taihō seemed minor; the flooding was quickly contained and the carrier's propulsion and navigation were unaffected. Taihō quickly resumed regular operations; however, gasoline vapors from the ruptured fuel tanks began to fill the hangar decks, creating an increasingly dangerous situation on board.

This is a running theme with Japanese damage control: they fail to ventilate vapor and purge fuel lines leading to increased risk of fire. And that's just what happened.

Hoping to clear the explosive fumes, an inexperienced damage-control officer ordered her ventilation system to operate at full blast. This action instead spread the vapors throughout Taihō, putting the entire vessel at risk. At approximately 14:30, an electric generator on the hangar deck ignited accumulated fumes, triggering a series of catastrophic explosions.

Boom.

For more on Taiho's loss, listen to Drachinifel's IJN Taiho - Always Train Your Crew and American and Japanese Damage Control in WW2.

USS Cavalla hit Shōkaku with three torpedoes and did great damage. Again, poor Japanese damage control and their rush to rearm were their doom.

Badly damaged, the carrier came to a halt. One torpedo had hit the forward aviation fuel tanks near the main hangar, and aircraft that had just landed and were being refueled exploded into flames. Ammunition and exploding bombs added to the conflagration, as did burning fuel spewing from shattered fuel pipes.

As at Midway, a Japanese carrier was hit while refueling and rearming its aircraft. All that fuel and explosives lying around greatly magnified the torpedo damage.

With her bows subsiding into the sea and fires out of control, the captain gave orders to abandon ship. Within minutes, total catastrophe struck the vessel. Volatile gas fumes had accumulated throughout the vessel, and when an aerial bomb exploded on the hangar deck, a series of terrific explosions simply blew the ship apart...

This is repeated time and again with Japanese carriers, most spectacularly at Midway where the US aircraft caught the Japanese rearming. Akagi is hit by a single bomb landing in a hanger filled with armed and fueled bombers. Their pumps and flooding systems failed and she was lost to fire.

Kaga is hit by three bombs, Sōryū takes the same, and Hiryū takes four. Bad damage to be sure, but recoverable. They both suffer fates similar to Akagi: armed and fueled bombers contribute to the damage, and their damage control systems fail.

In contrast, the USS Yorktown is hit by three bombs and an out of control dive bomber. But in anticipation of the attack they stopped all fueling activities, even dumping fuel tanks overboard. Fires in the hanger deck (also filled with armed and fueled aircraft) are quickly extinguished and she's able to resume fueling within 90 minutes. Salvage teams begin to repair the damage, but she takes two torpedoes from a Japanese submarine. She's abandoned, but remains afloat all night finally sinking in the early morning.

USS Hornet (CV-8) was also extraordinarily tough. Three bombs, two torpedoes, and a kamikaze knock out power. Despite this, power is nearly restored when another torpedo hits reversing all the repair work. With the Japanese on their way, the US puts nine torpedoes (many duds) and hundreds of 5 inch shells into Hornet. Still she does not sink. She finally goes down to four more Japanese torpedoes.