Yes, your data is safe if you run a properly configured ESXi system. Keep in mind that nothing is fool proof, your data can be at risk no matter what you do, hardware fails, electrical storms happen, fire happens. But ESXi and FreeNAS are designed to run together. How do I know this? Because VMWare Tools are built into FreeNAS.
There is some discipline that comes with virtuallizing all your VMs on one machine, you must shut down your VMs in the correct sequence. FreeNAS will likely be your first VM to power on and the last to power off. Give that some thought.
@examinor The one major piece of information you left out in your first posting was how much RAM your machines have, this is critical, also if you do or do not have an HBA add-on card. When you establish a VM for FreeNAS I personally give it 16GB RAM and that is "locked". No other VM can take this RAM away. I do run test FreeNAS machines with 8GB RAM but these are for testing alone as I try to locate bugs in newer software. I also create a 10GB vmdk drive for the boot drive for FreeNAS, this gives me the ability to have several boot environments for FreeNAS.
So lets say you have lots of RAM, now you need to have an HBA that you can pass-through your hard drives to your FreeNAS VM. I'm sure that you have more hard drives than SATA ports on your motherboard for all the drives you presently use in both machines.
If you are going to run an iSCSI setup then you can benefit heavily on significantly faster throughput and watch your other VMs run very fast with respect to hard drive speeds. Think of it like running a RAM Disk, while it may not be that fast, it can certainly come close.
My one warning is to not run a firewall on the same machine as all your other VMs unless you are a single guy and have no one else dependant on your internet. I made this mistake and now my firewall runs in a separate machine on top of ESXi and I have one other VM of FreeNAS as a backup for critical data from my main FreeNAS. I'd rather have an offsite backup but this is what I have right now.
I have a very long thread here "My Dream System, I Think" that might help you out. It is when I started using ESXi and I did a lot of testing and have a ton of advice from some very good people here. So if you wanted to read all the content, just search for it. And if you have any questions, ask away.
My last comment... You can use RDM to pass through drives and a few people are doing it reliably however I do not recommend this to anyone unless they understand the process and possible limitations. My backup FreeNAS machine has RDM drives however my main FreeNAS machine uses HBA pass-through. I just recently configured the RDM drives as a test and while it's early in my testing, it does appear to be working fine. Again, I don't presently recommend it but I'm also not going to hide this option from you.
If you have any question then please ask but also know that I'm not on these forums as often as I use to be. Life happens and it's keeping me pretty busy for the past several weeks and I don't see it easing up anytime soon.