It does actually seem to be a bit of a problem with a number of kits of this type of subject. My HMS Enigma is also a bit on the top heavy side, which is hardly surprising when you think that there are five additional white metal guns, one of which a 12 pdr, stuck to the top of the model.
You can allow for the weight in the ballasting phase of making the model but what you have to take into consideration as well is the stability of the finished item. Too much weight up top will make it slow to respond to heeling and then prone to shipping the odd wave as she hangs over. There is of course only so much weight that you can put in the bottom, limited by the designed load line, so remedies are limited to replacing the guns with alternatives made from resin or scratch built or removing weight from other areas of the model, such as reducing decks and bulkhead thicknesses, mast's etc.
At the end of the day it is up to the modeller and the individual model but I would recommend a lot of thought goes into the planning and design of this type of kit before committing to the construction. The Enigma is now fine and my own remedy was to ballast her a bit on the heavy side. This also has the effect of allowing water on the decks when it gets fresh but if you ensure the decks are sealed and the wash ports are free and she should be able to cope OK.