There's no difference in meaning between number one and number two. Number two is the one that's correct; number one would simply be regarded as an error. It's kind of like not putting a period at the end of a sentence.
The clause beginning with which is extra information that doesn't change the meaning of the sentence. Typically, when you have a nonrestrictive clause in the middle of a sentence, you place a comma at the beginning and at the end of the clause.
What bothers me much more than the missing comma is the use of whereas, which signals that you are comparing/contrasting two different ideas. I don't see that in your example.
Without removing whereas from the sentence it could be re-written a number of ways:
Whereas the ideas of X are conceptually explained and mathematically
formulated with the X theory, which navigates tradeoffs in sharing
context summaries among IoT devices.
Whereas the ideas of X—which navigates tradeoffs in sharing context
summaries among IoT devices—are conceptually explained and
mathematically formulated with the X theory.
Whereas the ideas of X (which navigates tradeoffs in sharing context
summaries among IoT devices) are conceptually explained and
mathematically formulated with the X theory.
Nonetheless, I think whereas should be removed, making it:
The ideas of X, which navigates tradeoffs in sharing context summaries
among IoT devices, are conceptually explained and mathematically
formulated with the X theory.
To me, that sounds much better.