Is there any effort made to keep the hydraulic lines for the different systems apart from each other on commercial aircraft?
Yes, and more than that. There is even an effort to determine more precisely what happens in case of e.g. an uncontained engine burst, and design the systems accordingly (either include segregation, or use other means to preserve functionality). It's called a Particular Risk Analysis.
Basically, a model is generated for physical events such as
an engine burst
all types of wheel bursts (like Concorde)
hydraulic accumulator burst
bleed duct rupture
and what not...
Typically, it's a collection of fragment trajectories and/or vulnerability volumes with various energy levels and sizes, depending on the scenario.
For each considered scenario, affected physical components (equipment, pipes, wires...) in the vulnerable areas are identified, and from there it can be determined how the aircraft and its systems will behave. If it's not acceptable, the design has to be improved.
For example, electrical harnesses carrying critical information are usually doubled in the forward fuselage (it can be one route in the floor, and a parallel route in the crown). In case of an engine burst, fragments may cut one or the other, but shall not be capable of cutting both routes at the same time.
It's not perfect, and by no means will the pilots have an easy day, but at least following such events there should remain sufficient functionality to bring the aircraft back on the ground