OK -- this begs three related questions: Is the short line that ostensibly operates these tracks owned by the local businesses that have lined up against the presence of the bike trails? It's difficult to imagine a RR corporation set up to simply run up and down the line without generating any online revenue unless it's simply a technical ruse by said businesses to "gaslight" the bike-trail concept. And second -- what is there about the presence of bike trails that has resulted in the businesses' opposition to their deployment -- is their development dependent upon track removal or, as the picture seems to illustrate, can the bike trail extend alongside the tracks? And the third -- are the opposing businesses in question planning to actually employ the tracks as part of their future businesses? If the rail-to-trail full-length concept was planned speculatively prior to actual acquisition or ceding of the rail property -- and, as described, the section in question is a "missing link" to connecting the dedicated ROW's seemingly desired by the trail advocates, then what's happening is an impasse. Bike trail supporters would need to legally prove that the operation of the track segment is not only unnecessary for the conduct of the business (and it's unlikely that the courts would accept simply statistical data regarding the commercial characteristics of the neighborhood) -- but that the current operation of that trackage is fraudulent. That'll be a tough one; as long as some cargo is being delivered or shipped from at least one of the on-line entities, the precedent has been to consider the line in use and thus "untouchable" from a legal or administrative standpoint. One would have thought that the planners of the rail-to-trail here would have had their ducks fully in a row prior to making promises about the complete deployment of their corridor. The old adage about making assumptions certainly applies in this instance! The trail may have to consider an alternate alignment in the vicinity of the trackage if some sort of agreement can't be successfully reached.
The tracks in question are owned by the Ballard Terminal Rail Company, named after the neighborhood they're located in.
According to Wikipedia, the company was formed in 1997 when BNSF abandoned the spur by the three remaining companies that were being serviced along the route. The article also states that as of 2008, only one company (Salmon Bay Sand and Gravel) still uses the rail line and this appears to still be the case today. However the rail company has expanded to two other short routes in the area, one between Woodinville and Snohomish, which is also the site of a proposed trail, and one in the Puyallup area, which appears to already have a parallel trail (I'm beginning to see a pattern here...)
Anyway, about the implications for trail development, yes, the track are actually legitimately used, though only at night so one would be forgiven for mistaking them as abandoned. However, the planners did indeed "have their ducks in a row" as you say since yes, the trail can go in alongside the tracks without necessitating removal, and the current iteration of the construction plans shows this, and previous ones did as well, as far as I'm aware.
The opposition of businesses in the area (both those using the rail line and not) seems to stem from not wanting a bike trail in the first place, which seems somewhat reasonable given the industrial nature of the area surrounding the missing link. However, their stated reason for opposition according to
this article from 2003 is concerns over "safety and liability issues inherent in the convergence of trains, trucks, cyclists, and pedestrians" but I'd think having a proper trail to formalize conflict points and crossings between bikes, pedestrians, trains, and trucks would be safer than the mess we have now! Of course I'm sure there would be an increase in bike/ped traffic but I'm sure there's already significant usage now what with the trail continuing on either end.
At any rate the point seems to be moot now since construction has started. The trail will alongside the streets of NW 54th St and NW Market St, and run along both the tracks and the street on Shilshole Ave NW and NW 45th St (where the picture is from). More infor on the project can be found
here.