What does the term "developmentally programmed" mean? I can't seem to find a definition anywhere.
What would the alternative (i.e. not developmentally programmed) imply?
The term could mean two things depending on the emphasis:
The first of the two appears to be the more common use of this phrasing if one wants to trust Google to be representative. Something along these lines might be intended in your example, though I don't see why this statement is necessary as it seems quite obvious that any organ that develops during embryogenesis is "developmentally programmed"...
I suppose the alternative ("not developmentally programmed") would imply that the development of secondary lymphoid organs is an accident which is not driven by specific mechanisms that exist for the particular purpose of developing them.
In any case, there is no magical scientific meaning to either of these two words, to me your example seems to be rather a mishap of phrasing.