Spin Seebeck effect (SSE) has been investigated in thin films of two Y-hexagonal ferrites Ba$_2$Zn$_{2}$Fe$_{12}$O$_{22}$ (Zn2Y) and Ba$_2$Co$_{2}$Fe$_{12}$O$_{22}$ (Co2Y) deposited by a spin-coating method on SrTiO$_3$(111) substrate. The selected hexagonal ferrites are both ferrimagnetic with similar magnetic moments at room temperature and both exhibit easy magnetization plane normal to $c$-axis. Despite that, SSE signal was only observed for Zn2Y, whereas no significant SSE signal was detected for Co2Y. We tentatively explain this different behavior by a presence of two different magnetic ions in Co2Y, whose random distribution over octahedral sites interferes the long range ordering and enhances the Gilbert damping constant. The temperature dependence of SSE for Zn2Y was measured and analyzed with regard to the heat flux and temperature gradient relevant to the SSE signal.