Hi Faisal,
I didn't find anything on the disadvantages of using secondary ip but the excerp below might help.
Usage Guidelines
This command first appeared in Cisco IOS Release 10.0.
An interface can have one primary IP address and multiple secondary IP addresses. Packets generated by the Cisco IOS software always use the primary IP address. Therefore, all routers and access servers on a segment should share the same primary network number.
Hosts can determine subnet masks using the Internet Control Message Protocol (ICMP) Mask Request message. Routers respond to this request with an ICMP Mask Reply message.
You can disable IP processing on a particular interface by removing its IP address with the no ip address command. If the software detects another host using one of its IP addresses, it will print an error message on the console.
The optional keyword secondary allows you to specify an unlimited number of secondary addresses. Secondary addresses are treated like primary addresses, except the system never generates datagrams other than routing updates with secondary source addresses. IP broadcasts and ARP requests are handled properly, as are interface routes in the IP routing table.
Secondary IP addresses can be used in a variety of situations. The following are the most common applications:
There may not be enough host addresses for a particular network segment. For example, your subnetting allows up to 254 hosts per logical subnet, but on one physical subnet you need to have 300 host addresses. Using secondary IP addresses on the routers or access servers allows you to have two logical subnets using one physical subnet.
Many older networks were built using Level 2 bridges. The judicious use of secondary addresses can aid in the transition to a subnetted, router-based network. Routers on an older, bridged segment can be easily made aware that there are many subnets on that segment.
Two subnets of a single network might otherwise be separated by another network. This situation is not permitted when subnets are in use. In these instances, the first network is extended, or layered on top of the second network using secondary addresses.
--------------------------------------------------------------------------------
Note If any router on a network segment uses a secondary address, all other devices on that same segment must also use a secondary address from the same network or subnet. Inconsistent use of secondary addresses on a network segment can very quickly cause routing loops.
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Note When you are routing Open Shortest Path First (OSPF), ensure that all secondary addresses of an interface fall into the same OSPF area as the primary addresses.
