There is no issue in submitting multiple EOIs. Many people do it in case they are not confident about claiming points and just want to get into the queue. But, it just doesn't seem right to me. I feel that it is not right for the same person submitting multiple EOIs under different email addresses. I think if you are confident about claiming your points, then you should go with one EOI. If there is confusion, then the DBIP will eventually raise that too. In my case, I updated my EOI but I did not open another one. I have seen cases where the applicants lodged visa applications in a rush and later got refused. It is better to wait, make your points right and then apply. It saves time and money. The entire process should be as clean as possible. The possibility of getting the visa is very high with less complicated cases.
One thing is ACS does not create many complications. In most cases, they accept the skilled experiences. But DBIP will thoroughly check and verify. So, even after ACS counts your experience, the biggest hurdle remains with DBIP.