1000 users is a pretty big broadcast domain. There will be a lot of broadcast traffic and a bad ethernet card can take the entire network down.
It is usually better practice to break up the address block into smaller networks and route. You can do this logically by department, room, floor, or building. VLANs can be handy for this. Then use a DHCP server for each network.
Divide the lot of users in multiple VLANs …my be 100/VLAN
Get an L-3 Switch to configure inter VLAN routing.
Define DHCP Relay on the L3 to direct DHCP broadcasts to the DHCP server (your Mikrotik)
This will definitely work without a hitch if a good NIC is installed in your mikrotik.
I know a network of 5000 users using a single PC running W2k3 as DHCP server. This works without issues. Mikrotik binaries are faster than windows ones. a Mikrotik DHCP should rock in this case.