What are the advantages and disadvantages on having a standalone HTPC with a standalone NAS server?
The standalone HTPC can be silent (or at least make less noise) if it has no spinning drives. The standalone HTPC can also be smaller if it has no 3.5'' drives.
You also get the usual advantage of standalone devices: you can upgrade and/or repair one without touching the other.
The advantage of a combined device is that it would cost you less, save you some time, reduce clutter (cables and whatnot) and perhaps consume less electricity.
If you go for separate devices, this should be done on the NAS:
Will also be using this as a torrent server, VPN service perhaps and maybe some lightweight logon scripts for my other PC's,
Is it hard getting a AMD A8 or core i3 very (not hearable) silent and cool in a smaller box?
So far as I know, it's hard to go much smaller than the HDPLEX without compromising on noise.
I don't know what fanless case if any would support the AMDs.
CPUs which are easier to cool such as the E450 are poor for gaming and might also be poor for some other application (I don't know what FlexAPP is).
But I don't think you need an A8. A less powerful Fusion CPU should serve you well and be easier to cool.
- power consumption (I know E450 uses very little, but based on what I've read its not too much of a difference from the other parts I listed when on load and in sleep. How much PSU power do I need for this?)
The E450 uses more than comparable Atoms but packs a better GPU. The CPU is poor but any computer with a comparable GPU will consume more power even if you underclock the CPU.
Any PSU will be sufficient for an E450 or the low-end Intel models. Even the more powerful AMD chips which are not very efficient will be content with fairly modest PSUs.
- price (this seems to go up a lot when choosing a standalone NAS)
It doesn't have to. Without the drives (which you would need in any case), you can build a basic NAS for a lot less than the price of an HDPLEX.
If you want one of the fancier models, it's a different story but those would also have advantages over a regular HTPC doubling as a server.
- heat (does a external PSU help?)
Yes, when compared with inefficient internal PSUs. Efficient internal PSUs are expensive.