No, it is because of how the different backup tools work as well as how the SysNAND is laid out. Essentially, your SysNAND is like a hard drive with multiple partitions on it (ctrnand, twlnand, and some other stuff) and the o3ds used a NAND chip of a certain size to hold it all. However newer systems often use a larger NAND chip (bigger hard drive) such as the 1.84GB one you have. However for backwards compatibility reasons, Nintendo doesn't use the extra space. Thus, your Sysnand consists of 1.21GB of space that has been allocated and is being used, and 0.63GB of space that is empty and will never be used (with one potential future exception, see below).
So tools like hourglass9 (or d9wip when doing a nandmin backup) don't do a backup of the entire NAND chip, but just the parts that have been partitioned/allocated which is why your older backups are 1.21GB. However GM9 (and d9wip when doing a full nand backup) will dump everything on the NAND chip, including 0.63GB worth of empty space (typically consisting of either 0x00 or 0xff, aka all zeros or all ones).
The catch is that while it is not finished/stable yet it is possible, thanks to cfw and other tools, to make the partition where dsiware is stored (twlnand) larger than what Nintendo gives you and have the extra space be usable. Thus, if you have a larger than stock twlnand partition, doing a "trimmed" NAND backup won't back up everything anymore. So backing up the entire NAND chip, empty space and all, is the easiest way to make it "future proof".
