You have to understand how silt is carried in water to understand the best way to deal with it in your situation. Silt is suspended in water. The more turbulent the water, the better it stays in solution. When the water slows or calms the silt falls out of solution.
Water moves fast in smooth pipes and the speed does not slow down if the pipe is at a constant pitch. A perforated pvc pipe (with the two parallel sets of holes) is designed to let water in and them give it a smooth valley to travel in order to carry the suspended material. The water filling up your stone trench is almost certainly not going to be moving faster than it will in the pitched pipe. That maens that the silt should remain in solution untill it leaves the pipe.
A corugated perforated flexible pipe is not going to have a constant slope, the ribs also slow down the water. It is much more likely that you will have silt build up in such a pipe. Putting a sock on the outside will keep silt out, but have you ever had any kind of filter that did not require cleaning or replacement to be effective? Instead of the pipe clogging, the sock clogs. Neither is a picnic to replace.