Why storage size of pen drive is less than given size

What pen drive and specific situation are you referring to?

There are several situations resulting in usable storage less than native capacity. For example, if a large drive is formatted with a file system, such as FAT-16, that has an inherent volume size limit less than the drive capacity, there will be unused capacity. Another common source of confusion is the discrepancy for storage products between the advertised capacity defined in millions (1,000,000) or billions (1,000,000,000) of bytes and the true megabytes (1,048,576 or 2^20) or gigabytes (1,073,741,824 or 2^30) reported by the computer. A drive advertised as 8 GB (8,000,000,000) would be only 7.45 (8,000,000,000/1,073,741,824) actual gigabytes.

Officially 1GB is 1024MB and that is how windows will see it, factories say that 1000MB is 1GB so although if it's a 2GB drive (2000MB) windows will see it as 48MB under 2GB

In other words, you can buy a house with so much square feet but the furniture is going to make it look smaller.