Is it permissible to benefit from the services of websites that resell e-commerce and design tools, whether bundled or individual, at a cheap monthly price, while not knowing the permissibility of how these websites obtain these services?

If the websites own these programs or are authorized by the original owner to sell them, then there is no harm in that. However, if they are pirated programs whose owners have not authorized their copying, then it is not permissible to purchase them from these websites, because that is considered anointing the rights. If you do not know, then there is no harm.