"n'en est pas moins" is a construction which means something is surprising if we refer to what we know of the context.
"Il sait que fumer est mauvais pour lui, il n'en continue pas moins à acheter des cigarettes."
"He knows smoking is bad for him, yet he keeps on buying cigarettes."
So it is (more or less) an equivalent to "yet", I think.
"en" refers to the context of the sentence, it links to the reasons which explain why this decision (destroy the Bastille) is surprising.