I think you're correct. They were having troubles. . I'm sure some other boats have issues somewhere, but no where near that bad.
In Nekton's case, they had financial management issues and maintenance issues (which are usually because of finance issues). So the ships had problems, trips were canceled, and when trips were canceled, the company doesn't make money and neither does the crew (on tips). It ends up being a bad day for everyone.
In the end, Nektons financial issues were their demise. They are now no longer in business.
I think people/customers prefer Credit Card payment because it's easier/convenient to them. Now days most folks prefer not to carry $200-$1,000 in cash. However, the liveaboard crews prefer cash any day. (can't say I'd blame them).