I cannot comment on the MX200, but this behaviour is observable on a lot of budget SSDs.
The sector ranges that contain actual data have a much slower read speed than the empty (and TRIMmed) space, which basically reads at line speed.
I have seen this on the MX100 as well.
I could not observe it on the 840 Pro for example, not matter how full it was or how much I tried to fragment it internally.
Because HD Tune is a program initially created to benchmark HDD not SSD. Did you try increasing the block size to something like 2 Mo ?
I'm sure your ssd is fine but if you want to be sure, make real tests like coying large files from and to the ssd maybe with a ramdisk if you don't want to be speed limited.
It's funny that people think that benchmarking a drive should always give "the real picture" when it's often not the case. E.g. 840 EVO owners with rapid enabled thinking that everything is blazing fast but in reality (and with the infamous bug) it's much slower, or in OP's case it's the opposite.