To change this behavior, follow these steps.

First, temporarily remove any other input sources used for languages other than Japanese:

1. Open System Preferences.
2. Select Keyboard.
3. Select the Input Sources tab.
4. Select a non-Japanese input method in the list. 
5. Click the Remove Input Method button (-) to remove the selected method.
6. Repeat steps 4 and 5 until you have removed all non-Japanese input methods.

Next, remove the associated preference file for Input Sources.

1. From the Finder, hold down the Option key and choose Go > Library.
2. Open the Preferences folder in the window that appears.
3. Locate the com.apple.HIToolbox.plist file in the Preferences folder. Drag this item to the Trash.
4. Restart your computer.

Finally, re-add any of your preferred input sources using the Input Sources tab of the Keyboard preferences pane of System Preferences. 

1. Open System Preferences.
2. Select Keyboard.
3. Select the Input Sources tab.
4. Click the Add Input Method button (+) to add the input method you want to use.
5. Select your input method from the list, then click Add.
6. Repeat steps 4 and 5 until you have added all of the input methods you want to use.

The Hiragana input source should then be available as an Input Sources option.