Hiya Jan,
Oh my!

You get extreeeemley lucky in finding parishes listed for Scottish born people on an English census but then have a very unlucky collection of names as they are very common.
Okay a couple of thoughts.
Thom
Pson I believe is considered the "english" spelling and Thomson the scottish. The latter is more frequent in the SW of Scotland. So they maybe either but an english enumerator automatically puts the P in.
Janet is ~ 19 when she has William. Chances are he'll be the first obviously not assuming as much. Therefore I would hazard a guess that she was married between 1840-1842 if she was married at all (Kirkcudbright & Dumfriesshire had teh highest illegitimacy rate in the UK in 1831).
The IGI has a really good coverage for marriages for Annan and Dumfries. I think you should try a male Thom(p)son with a female Janet marriage on all the batch numbers fro Dumfries and Annan. See if you can flush them out that way.
The births of the boys maybe available on Scotlandspeople, there are no boys births on IGI. But that is pay per view. The Dumfries OPR only gives father's names so it would be hard to cross reference fo rthe mum.
As John was born in 1849 in England that suggests they aren't in Dumfriesshire in 1851. 1851 census is available free online here...
http://www.dumgal.gov.uk/HistoricalIndexes/default.aspxIn 1841 Janet could be...
1. In Annan unmarried
2. Working in service (very common) and therefore at an unknown location with an unknown surname and one of the most common first names in Scotland - ouch

3. Married in Annan or Dumfries or somewhere else.
I have some Dumfriesshire 1841 name indexes.
I looked in Annan for a married Janet
- no luck

for Thompson or Thomson
I looked in Dumfries Burgh for a married Janet
- no luck

for Thompson or Thomson
Well not of the right age anyway and I was generous.
I would suggest trying to find
a) Possible marriage on IGI
&
b) Birth details of either Henry or John. These will be statutory registrations rather than the hit and miss OPR. It will also give you the maiden name of Janet then I'm sure we'll get some luck with 1841 for Janet.
Annan records are in general quite complete though they get ropey in the 1820s but I still think there is a better than average coverage. My 4xggrandfather was married in Annan in the 1820s and the entry looks liek it is written by a drunken monkey! But it's there

Hope this helps,
Pam