Definitely. There are ethical concerns. Firstly, it might not be in line with the moral standards of a large part of the audience. Secondly, it could potentially lead to the misuse of the visual novel's content for improper purposes, rather than respecting the work as an art form. In addition, it may also have a negative impact on the reputation of the visual novel industry.
One way is through industry self - regulation. Visual novel developers and publishers can set their own standards and guidelines to prohibit or restrict the use of nude filters. Another way is through legal means, such as having laws that clearly define what is acceptable and unacceptable in terms of content modification in visual novels.