The true answer may involve a personal matter which will never be exactly known. Fortunately, the OP's actual problem is understanding why this gratitude would even exist. They ask, "So what could it be? To this question, there is a very logical answer involving Aquaman's Newfoundland production unit:
Hypothesis 1: There happens to be an accident while filming in Australia and one of the Newfoundland crew is taken to the hospital. The family in Canada is notified and needs to immediately fly to Australia to be with their loved one.
Hypothesis 2: Digital editing in Newfoundland ran longer than expected and some employees need to work longer than 6 months.
Both of these situations would likely need help from the Dutch Ministry of Defense's (DMD).
Obviously, this opens more questions. Why would a Canadian family need the DMD help to fly a family to Australia, or to work longer than 6 months?! Really??
Yes, really. But that is a great question! And odd as it seems the answer is very logical and even probable.
In short the Canadian film industry - and Newfoundland in particular - simply has and actively employs a large population of Dutch citizens who would require specific visas and passports to travel internationally while working on this project. Such documents are issued by the Dutch Ministry of Defense (DMD).
Canada has established free trade with The Netherlands through a Comprehensive and Economic Trade Agreement (CETA). Dutch citizens can work in Canada for up to 6 months without a work visa. To the Dutch Canada is a land of opportunity. In fact both nations are trying to make themselves mutually visa exempt by 2020. This generates a lot of migration from Netherlands to Canada. It's free, after all, and Canada has tax-exempt jobs!
One of the unintended negative consequences of the heavy Netherlands-Canada migration is what the DMD refers to as "brain drain." The Dutch consider this a serious national security threat. What is that? Specifically, on page 5 of The Hague Center for Strategic Studies reports that
The Netherlands suffers from brain drain to Canada, which remains the
top destination chosen by the highly-skilled migrants migrating from
Because of this threat, the DMD looks very closely at work visa applications and has to consider if granting one may hurt the nation. Certainly, an application is not casually "rubber stamped."
So what highly-skilled Canadian jobs are Dutch citizens taking?
Canadian Government Creates Incentives For Film Industry Jobs
Newfoundland and Labrador specifically are suffering an unemployment crisis with over 13% unemployment in 2017. This is forcing them to create great incentives to invest in Newfoundland industries, specifically film industries. The Newfoundland and Labrador Department of Finance has established a tax-exempt corporation, the NLFDC. This company was literally formed by the provincial Canadian government for the mission of promoting Canadian film industry:
The NLFDC has been mandated to promote the development of the indigenous film and video industry in the Province, as well as to promote the Province in national and international film and video markets
The NLFDC literally makes film production in Newfoundland and Labrador completely tax exempt - including payroll for cast and crew.
The combination of film incentives, free trade with Netherlands, and an ample population of highly-skilled Dutch citizens who don't need visas to work means it is almost certain this film employed several Dutch citizens in their Newfoundland unit.
Why the DMD is involved: All Dutch visas and passports are issued and managed by the DMD.
A Dutch employee reached the end of his/her 6-month visa exemption during production, requiring them to get an emergency work visa from the DMD.
Human trafficking is a serious problem for the Dutch, as such they are very proactive in preventing international child abduction. A Dutch minor who needs to travel internationally MUST get the DMD to directly authorize children traveling internationally.
Again I think you won't get a complete list of employees on this project with their nationalities conveniently displayed, but it's not at all unusual that many people working on a very lengthy Canadian film were dutch and as such needed special consideration for travel. If you read the entire credits through you will see several dutch names in the Newfoundland unit. Those are very likely not Canadian citizens, and the DMD would have to grant visas and passports as necessary for their citizens to work on this production beyond their 6 month exemption or take their children to Australia, italy, or Morocco.
Additionally the OP mentions the possible use of Dutch military vessels in production. At this point that is pure speculation, however once again it would not be unusual for Dutch equipment to be used in a Canadian production due to CETA. The Dutch do have a military presence in Canada mostly to assist the ageing Canadian defenses. One possible but unlikely way the DMD would need to assist the Canada unit would be to carry a film crew or mounted a camera on a helicopter. Canada doesn't even own military helicopters, the Dutch have AH-64 Apache helicopters deployed. This again is pure speculation and seems unlikely.