Yes, RTL and LTR kerning are stored separately now. And the old kerning s not compatible with the new way anymore. Each kerning is only visible in Window > Kerning if the current tab is set to the respective writing direction.
To convert ‘Glyphs 2 old-style mixed kerning’ to ‘Glyphs 3 direction-aware kerning’, use the mekkablue script Kerning > Convert RTL Kerning from Glyphs 2 to 3:
