im using nilaus' reactor design and before bobs logistics it was producing more than 450MW, but after bobs its only making 160 (im only using 2 of the 4 reactors) the heat exchangers arent getting water even though the off shore pumps are pumping into tanks which have pump 4's pumping into the network, the pipes arent carrying the water, and the heat pipes arent transferring heat either! the exchangers used to get to 900+ degrees now just barely 500. is this a bug or is this really how the mod is supposed to work, and by that i mean for it to not work in an intuitive manner....

Can you post a screenshot of the design please? Also what tier of Reactor, Heat Pipe, Heat Exchanger, and Turbine are you using?

Simply adding Bob Logistics shouldn't change anything related to nuclear power in any significant way. The only change that would really effect anything is the changes to the pumps, you'd need to upgrade from the base game one to a MK4.

Other mods like Bob power could change a few things too, including the temperature that the heat exchanger runs at, but if everything is already running, shouldn't effect anything either.

The only one I can think of that could effect anything is if you add Bob Revamp if you have Bob's Metals Chemicals and Intermediates and Bob's Power installed. it locks a specific reactor to use a specific type of fuel cell, so if you have the wrong fuel cell in the reactor, it would stop working.
You'd have to take it out of the reactor (at which point it won't let you put it back in) and put the right type of fuel cell back in.

Bob Revamp does have an option to turn off Nuclear Overhaul that should allow you to put all fuel cells in all reactors again.