Running the Juniper Client in Boot Camp is exactly like running it on a 'real' PC because when running Windows in Boot Camp the Mac is a real PC. So yes the Juniper Client will work as well as it would in Windows on a real PC.
What Boot Camp will not do is let the Mac side of things use the Windows VPN client. With Boot Camp the Mac and Windows environments are totally separate with only one running at a time. If you want to run both Mac and Windows at the same time you should look at wither VMware Fusion or Parallels.