This question includes an interesting observation and is one that every country that grows GM crops asks. Regulating agencies are very interested in making sure GM crops are compositionally the same as non-GM and that the gene does not negatively affect the plant. As you point out, honey production is an important aspect of canola production, and thus companies make sure that the plants used to develop GM varieties will still produce nectar. Canada is the second-largest grower of canola (the European Union is first), and 90 percent of the Canadian crop is GM. Dr. Medhat Nasr, Alberta provincial apiculturist, Pest Surveillance Branch, made the following comments about honey production in canola in Canada:
“In Canada, we grow about 19 million acres of canola. For acreages of canola, please check http://www.canolacouncil.org/markets-stats/statistics/harvest-acreage/. Canola as a crop is mostly self-pollinated, with little cross-pollination. When bees are placed in canola fields, canola yield increases by about 15 percent.
“In Alberta, Saskatchewan and Manitoba, about 90 percent of honey comes from canola. The average honey production per hive is 140 lb, 200 lb, and 190 lb, in Alberta, Saskatchewan and Manitoba, respectively. However, it is clear that canola produces nectar. What we are seeing in these provinces is an increase of cultivated acres with canola, due to high prices for farmers. This increase is taking away acreage from clover and hay that used to be the main sources for honey. Clover used to produce nectar at two times—one time in early summer, and the second time in late summer—based on two cuts. Therefore, beekeepers used to harvest more honey from clover. Now we find that most harvested honey is only from canola and from only one harvest. This is the nature of changing agriculture around us, and the reality of farming.
“For pedigreed hybrid canola for seed production, honey bees and leaf cutter bees are used for pollination. This type of crop is dependent on bees for pollination as a part of the four-way breeding system. This type of canola is grown as male flowers and female flowers in different rows. Bee pollination will contribute 90 percent of seed yield to this crop. No significant honey is produced in these fields, due to high density of number of hives per acre (not enough nectar available for all of the bees in the field). However, beekeepers receive good compensation for pollination services, approximately $180/hive. This info might also explain why average honey production is low in Alberta, due to renting over 75,000 bee colonies for pedigreed hybrid canola for seed production. These hives produce, on average, about 40 lb honey/hive.