It shouldn't cause an issue because the license will not be accepted if there are features in use above those for which the license is entitled. vSAN does entitle you to use a vDS, so not sure why you'd be getting that warning if you have a valid license applied (unless expired, maybe).
I have a similar setup where vCenter and ESXi has standard license and we have applied vSAN license to the cluster but I haven't received such message before and the setup with vDS is working fine.
Maybe it's normal and you won't face issue while working with vDS and vSAN. Have you tried adding the host in vDS and faced any issue ?
Yes that is my understanding that applying a Standard License to an ESXi which is part of a vSAN cluster (with Standard vSAN license) should not list the Distributed Switch as unsupported. Because of this warning I was worried it might all of a sudden disconnect the host from the Distributed Switch and causing connectivity issues to underlying VM's