I suspect the cruise ships are leery of all sorts of mandate and possible quarantine issues (i.e. State and Local) as well as concerned with the degree of increased cleaning, spacing, etc. Back in July, the 1st cruise came into JNU with, IIRC, 680 passengers vs. 2200 pax capacity.
There's also some non-Covid stuff like the (recently defeated, IIRC) ordinance in Juneau that would have impacted the number of ships allowed in at any one time.
...and they may be having staffing issues like many similar hospitality sectors: Denali Princess Lodge is closed this year (although, with the tie-in to Princess, that closure is a chicken or egg debate), K2 is offering reduced # of tours, Simon & Seaforts is running at circa 60% capacity, etc.