No you will not -
vmxnet 3 is a new virtual adapter added to ur vSphere 4.0, it is recommonded to have updated virtual hardware for better performance. however you can continue to work both vmxnet 3 & e1000. you will not face any compatability issues.
We have ESX 4.1 with 14 hosts in our environment.
Initially we had VM's are configured with the e1000 NIC adapter only.Later on we added 100's of VM with vmxnet3 NICs.
We are'nt faced any compatability issues so far.