As a chemist that develops cleaning products let me talk about linseed oil for a minute. Linseed is basically flax seed oil. It is composed of fatty acids like linoleic and oleic acids. This means you can eat it, like any other vegetable oil. It is nutritional for humans, animals and of course mold.
Where Linseed oil is different than say canola oil is its ability to polymerize. Contrary to what people think, linseed oil does not evaporate or loose any of the oil as it "dries" The molecules undergo polymerization where many small molecules join together to make very large ones. This changes the material form a liquid to a semi-solid. The polymerization degree will vary greatly depending on the quality and age of the oil and what additives are in the oil (catalysts).
Now to the mold problem: When you have "dried" linseed oil in a dry environment, mold is not able to "eat" the oil because of the molecular form of the oil. But, when you keep it wet for an extended period of time, and especially if it is warm and dark, the oil will start to break down and some of it will get rancid (oxidized) just like you can get rancid butter. This is perfect mold food. So under canvas equals wet, warm, dark and add a source of mold food and you have the best possible place to grow mold.
How to get rid of the mold? Well, unfortunately, the linseed penetrates far into wood. You can bleach the color of the mold away using say chlorine bleach, but the mold is already established inside the wood where nothing can get to it. If it gets wet again, the mold will return. As far as I know there is no know way to permanently remove mold from a porous surface. You could try to get as much of the linseed oil off as possible, using say mineral spirits or another solvent, but I doubt you could ever get it all out of the wood.
On anti-mold compounds. I have not researched what is available to consumers. However, they are used extensively in various professional formulas. The compounds that are affective against mold are also extremely toxic to humans. I'm not afraid of chemicals and I suit up, wear gloves and work in a fume hood if possible when using them. Be careful with any anti-mold compounds.
In conclusion, I would never put linseed oil on anything that will ever get wet for any length of time, especially a canoe.
edited for clarity.
