Is there any specific reason for having all VLAN info only in VLAN.dat file?.Though we are configuring it manually then why can't we see it in Running-config?
The vlan.dat file provides a permanent storage for VLAN configuration independent of running-config and/or startup-config. If your switch participates in a VTP domain, the changes to the VLAN configuration (VLANs, their IDs, names, states and other properties) may change over time as modifications are made. Bear in mind that a switch never saves the running-config to the startup-config on its own. If all VLAN configuration was present only in the running-config, it would be necessary to manually copy the running-config to startup-config on every switch in the VTP domain after each VLAN database modification, otherwise the changes would be lost after reboot.
The vlan.dat solves this problem. The switch is allowed to overwrite the vlan.dat automatically after each VLAN database modification, independently of the runnning-config. This makes it safe to modify the VLAN database without worrying that some changes are being made to the running-config, and without needing to save it to the startup-config over the entire VTP domain.
Note that when you configure the switch to the VTP Transparent mode, all VLAN configuration in fact appears in the running-config as well, although it is still maintained also in the vlan.dat file. It is consistent with the description above - a VTP Transparent switch does not participate in VTP domain and thus no external modifications to its VLAN configuration will take place, so there is no problem in maintaining the VLAN config in the running configuration.
This is how I see it.