Zelda isn't as popular in Japan compared to the rest of the world. I'm not 100% sure on FE being more popular though, like haven't most Zelda games done 300k LTD in Japan? That's about the ceiling for most FE games too. And BotW will definitely sell more LTD than FE Switch, no matter how good FE Switch is.
300k is more low end for Zelda in Japan.
Famitsu
Ocarina of Time (1998) 1,143,570
Links Awakening DX (1998) 314,309
Majoras Mask (2000) 601,542
Oracle of Ages (2001) 373,352
Oracle of Seasons (2001) 372,690
The Wind Waker (2002) 742,609
A Link to the Past DX (2003) 293,989
The Minish Cap (2004) 235,400
Twilight Princess (2006) 554,109 + 70,000
Phantom Hourglass (2007) 902,386
Spirit Tracks (2009) 740,109
Ocarina of Time 3D (2011) 636,571
Skyward Sword (2011) 349,143
The Wind Waker HD (2013) 66,445
A Link Between Worlds (2013) 454,306
Majoras Mask 3D (2015) 469,082
Twilight Princess HD (2016) 93,489
Breath of the Wild (2017) 569,658 + 125,915
vs FE
Genealogy of the Holy War (1996) 486,000
Thracia 776 (1999) 158,695 *not including NP release
The Sealing Sword (2002) 345,574
The Blazing Blade (2003) 265,286
The Sacred Stones (2004) 346,719
Path of Radiance (2005) 156,413
Radiant Dawn (2007) 171,924
Shadow Dragon (2008) 252,309
Heroes of Light and Shadow (2010) 250,592
Awakening (2012) 484,521
Fates - Birthright/Conquest (2015) 581,905
Echoes: Shadows of Valentia (2017) 208,932