Unless I'm missing something, I don't see any functional point in capping those ends if you aren't using this line. All this is is a line direct between the turbo inlets on either side to help balance out pressure between the inlets just in front of the turbos. I guess you can cap the ends to keep dirt out in case you use the line again in the future, but capping the ends is safe and not going to change anything since you don't have these lines any longer.
Now whether or not this pressure balancing is needed or not is a whole different debate. I don't recall exact details, but I think depending on turbos it was kind of an extra. Might be some other threads out there on the topic if you want info on that and are rethinking your choice of inlets.
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