Because "kilos" already had a meaning outside of computer file size, but "megs" did not. So we understand "megs" to be megabytes, but "kilos" is usually a measure of weight. So there was a different shorthand for "kilobytes".
Now, maybe I'm the minority here, but I've not heard many people use the shorthand "K's" for kilobytes, but I have heard "kb's" as a shorthand, and "kb" would be pluralized in the same way as "megs". "Forty kb's" is definitely something I've heard before.
Similarly, we would not say "The file is forty Ms", which would be parallel to forty "K's".