This is because in their default styles, the font size is not set via TemplateBinding. See the ** part, that should do the trick. :)
<Style TargetType="toolkit:DatePicker">
<Setter Property="Background" Value="{StaticResource PhoneTextBoxBrush}"/>
<Setter Property="BorderThickness" Value="0"/>
<Setter Property="Foreground" Value="{StaticResource PhoneTextBoxForegroundBrush}"/>
<Setter Property="HorizontalContentAlignment" Value="Left"/>
<Setter Property="PickerPageUri" Value="/Microsoft.Phone.Controls.Toolkit;component/DateTimePickers/DatePickerPage.xaml"/>
<Setter Property="ValueStringFormat" Value="{}{0:d}"/>
<Setter Property="Template">
<Setter.Value>
<ControlTemplate TargetType="toolkit:DatePicker">
<StackPanel>
<ContentControl ContentTemplate="{TemplateBinding HeaderTemplate}" Content="{TemplateBinding Header}" Foreground="{StaticResource PhoneSubtleBrush}" HorizontalContentAlignment="{TemplateBinding HorizontalContentAlignment}" Margin="12,0,12,-4"/>
<Button x:Name="DateTimeButton" BorderThickness="{TemplateBinding BorderThickness}" Background="{TemplateBinding Background}" Content="{TemplateBinding ValueString}" Foreground="{TemplateBinding Foreground}" FontFamily="{TemplateBinding FontFamily}" HorizontalContentAlignment="{TemplateBinding HorizontalContentAlignment}" Height="72" **FontSize="{TemplateBinding FontSize}"**/>
</StackPanel>
</ControlTemplate>
</Setter.Value>
</Setter>
</Style>