Offset in the sense that Japan was importing much of the whale caught by Iceland, and will simply be catching more themselves now.

If we were farming whales maybe your cow comparison would have any kind of relevance, but we're not. When more whales are caught there isn't anyone who's breeding more whales to compensate. And unlike farm cows whales have been an important part of the ecosystems they interact with for millions of years. Also, Japan doesn't only hunt minke, and are caught hunting endangered whales regularly. Many of these are keystone species and there will be significant consequences to ocean ecology if they disappear.

Things are already bad from overfishing of all kinds and the decimation of whale populations by the absolutely monsterous amounts caught through the 20th century. And it's going to take a long time for ecosystems to recover even without Japan ignoring international law and the warnings of every expert on the planet.