On boot, whenever netifd is restarted, upon calling ifup or ubus call network reload. However the switch related portions of this config are actually processed by the swconfig executable which is triggered through the network init script.
Yes, via netlink. You need to use the equivalent of what ip link add link eth0 name eth0.100 type vlan id 100 does internally. If eth0 happens to be wired to an swconfig switch, you need to program the switch IC via swconfig (or its internal netlink apis) as well.
After making the appropriate netlink calls roughly equivalent to ip link add link eth0 name eth0.100 type vlan id 100; swconfig dev switch0 vlan 100 set ports "a b c d"; swconfig dev switch0 apply, the config should be effective immediately.