http://www.ecologie.gouv.fr/article.php3?id_article=3569
so it does seem that "soutes" are taken into account for emissions. but i am not sure about the translation
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Les soutes aériennes et maritimes
vendredi 4 février 2005

Même si elles ne sont pas comptabilisées dans les inventaires nationaux Kyoto, les émissions de GES des « soutes internationales » aériennes et maritimes doivent aussi faire l’objet d’évaluations plus précises, surtout dans le cas du transport maritime, mais aussi de mesures volontaristes de réduction. Les émissions du transport aérien international au départ de la France ont augmenté de 72% entre 1990 et 2003. Les actions de maîtrise des émissions relèvent d’une coopération entre la Convention climat (CCNUCC), l’organisation maritime internationale (OMI) et l’organisation de l’aviation civile internationale (OACI), trois organismes de l’ONU. La France élabore des propositions concernant l’aérien, qui seront portées au niveau communautaire, l’Europe se voulant pilote en ce domaine.

Evolution des émissions de GES « soutes internationales françaises » de 1990 à 2003
MteCO2 1990 2000 2001 2002 2003 2003/90
Air 8,6 14,4 14,6 14,7 14,8 +72%
Mer 8,1 9,6 8,2 8,0 8,7 +7%

Source CITEPA décembre 2004

It looks like they're talking about international storage tanks - see this part of the kyoto protocol

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Note added at 13 mins (2005-11-03 16:30:30 GMT)
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The Canadians use "international bunkers" in their translation :(

Google has plenty of examples

Climatic Change of the Second Chamber of Par-. liament held public hearings and made other ... Air and marine bunkers also contribute to emis- ...

Ministère de l'écologie et du développement durable : Le Plan ...Les soutes aériennes et maritimes (4 février 2005) ... afin d’atteindre les objectifs du protocole de Kyoto sur la lutte contre le réchauffement climatique.

Mission Interministérielle de l'Effet de Serre - Qu'est-ce que l ...... de gaz à effet de serre des soutes internationales aériennes et maritimes. ... La prochaine conférence de l'ONU sur le réchauffement climatique aura ...

Like "bunker", "soute" (including "soutes" in the plural form) has two meanings:
1) the hold or bunker in which something is stored
2) bunker fuel, i.e. the fuel used by ships.

soute
1. Dans un navire, compartiment fermé ...
2. Compartiment à bagages aménagé dans le fuselage d'un avion
3. n.f. pl. Combustible liquide pour les navires.
[Larousse Lexis]

bunker - A storage container for solid fuels or a compartment on board ships for storing fuels

Bunker B, Bunker C. See heavy fuel oil.

bunker oils. Heavy fuel oil, stored and burned on board ships.
[Dict of Energy, Macmillan]

I'm sorry if I'm stating the obvious, but I was far from sure that this was clear or understood in the discussion above.

Why they could not have assigned each ship's country of registration the corresponding volume of pollution I don't know, but for whatever reason consumption and emission by shipping is recorded separately.

"Bunker (oils)" is undoubtedly as clear to the English-speaking reader as "soutes" is to the French. Up to you whether you translate it that way or go into a little more detail for the non specialist, along the lines of "shipping".
1)

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Note added at 5 hrs 13 mins (2005-11-03 21:30:15 GMT)
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Ship emissions are getting worse faster than other sources of pollution are getting cleaned up
http://www.westport.com/news/view.php?table=tLind&id=67&retu...

I'm obviousl not the only one surprised that these emissions are not assigned to countries:

Reducing atmospheric emissions from ships is a high environmental priority for the European Commission. A recent emissions quantification study for the Commission suggests that by 2020 ships in EU sea areas are likely to emit as much acidifying air pollution as all land-based sources combined
[…]
Under this task, the contractor should make preliminary annual assignments of ship emissions to EU Member States, acceding and candidate countries. The emissions to be assigned are sulphur dioxide, nitrogen oxides, volatile organic compounds and carbon dioxide. The seven different approaches below should be used, plus at least one more which the contractor should determine themselves.
A.
Assignment according to location of emissions
Estimate how much is emitted by seagoing ships in each country’s waterways, ports, 12 mile territorial waters, exclusive economic zones and pollution control zones, where such zones have been claimed. To the extent possible, disaggregate results by area, and by type of ship movement (domestic / intra-EU / international; inland / seagoing).
europa.eu.int/comm/environment/ air/pdf/nec_techn_annex.pdf