There were a few dots like that on my Sony PRS 505 but I haven't noticed any on my Kindle DX.
Like you said they were really only noticeable when cleaning the device and they didn't bother me while I was reading.
I am really picky about stuck pixels on LCD screens but the small dots on the e-ink display didn't bother me enough to get an exchange. Since the e-ink spots aren't lit up they don't really stand out.
If you decide that the dots do bother you Amazon would most likely exchange the device for you without any hassle.