Here is an example of work of academia on fisheries subsidies prior to 2001. It concerns an article published by Gorazd Ruseski in the Journal of Environmental Economics and Management (Volume 36, Issue 1, July 1998) titled "International Fish Wars: The Strategic Roles for Fleet Licensing and Effort Subsidies" . I quote here from the conclusions of the article:
The effort subsidy and fleet licensing models developed in this article depend on the credibility of the strategic choices made by countries. Widespread evidence of excessive subsidization and licensing of large fleets makes it clear that these commitments are credible indeed. However, as discussed in a report prepared by the New Zealand Fishing Industry Board [20, p. 41], it is relatively much easier to consider subsidies as a strategic policy used to help a fishing industry, as opposed to other industries, because “The call for subsidies to the fishing community in North America (much of which is seen as a form of ‘disaster relief’) seems to engender an emotional response within the population and to be acceptable to both state and federal politicians.” Also, Shrank  note that many countries are unwilling to reduce the sizes of their fishing fleets, because fisheries are often thought of as an “employer of last resort” in many small coastal communities that depend on them.
20. Seafood Trade Access Study, N. Z. FIB, Wellington (1996).
22. W. E. Shrank, N. Roy, R. Ommer and B. Skoda, An inshore fishery: a commercially viable industry or an employer of last resort?. Ocean Develop. Internat. Law 23 (1992), pp. 335–367.
This paragraph is remarkable as it contains a number of elements directly pointing to what is now happening in the WTO negotiations:
1. The reference to New Zealand's industry report on "Seafood Trade Access" of 1996. Note that it is as early as 1997 that New Zealand started making submissions at the WTO on fisheries subsidies.
2. The notion of "disaster relief", which is being used (following a submission by the U.S.) in the draft negotiating text issued by the Chair in November 2007.
3. The quotation from a paper from Shrank in which he notes that many governments consider fisheries as an “employer of last resort” in many small coastal communities that depend on them. This seems to reverberate in the negotiations when discussing the need for more flexible disciplines for "artisanal - samll-scale - subsistance" fisheries.
As a final comment I would like to underline that Gorazd Ruseski is one of the offcials that testified in one of the hearings at the Canadian Parliament on the ongoing WTO negotiations on fisheries subsidies.