In normal case management agent restart wont affect the running VMs. The host will be disconnected from the vCenter server for a while and will be reconnected automatically once the management agent is started running. During this time all the VMs will be grayed out in vCenter server.
Also it will disconnect the direct host connection through vSphere Client if there are any.
Its recommended to put the host into maintenance mode before restarting the management agent or the host itself. Because in ESXi 3.5, 4 and 5 there were instances the hostd stuck will starting due to the SCSI errors in storage or the APD.
Though APD and storage errors are well handled in 5.1 I would suggest put the host into maintenance mode and do hostd restart.