The topic is so iffy and the debate is so heated. The pro skimmer people will tell you that if the skimmer is producing no bubbles than it is fine. The con skimmer people will tell you that any skimmer on a horse tank will increase the likelyhood of GBD is a seahorse that is prediposed to it. For me the skimmer whne it's running is in the sump.
Have I run a skimmer on a seahorse tank yes.
Have I ever had disease no.
Do I think the safest way to run a skimmer on a horse tank is in the skimmer, yes.
Is it a descion you have to mkae for you, yes.