Dear Arghya,
we finally could look into your questions.
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Generally, the secondaries will have the Q(LET) values applied as well. The Q(LET) value is mainly contributing for hadrons or other heavy particles but not for electromagnetic particles. This means that you only see a non-negligible contribution if the impacting proton beam has a high enough energy, where it can create a hadronic shower.
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The Q(LET) in FLUKA is calculated using the definition given in
Table A-1that can be found in theICRP60 International Comission on Radiological Protection, ICRP Publication 60, Annals of the ICRP 21, 1-3 (1991), also discussed in this post.
Cheers,
Barbara