I don't have a 3D TV, so I can't directly answer to the question of playing 3D BD ISOs directly from HDD, but... All the movies I have in BD format are in 500Gb external HDD's.
I found this for myself, a very simple way of watching BD movies from external HDD's without making long conversions of files
When I "unrar" a movie, 99% of the times I get 2 folders, as probably all of you are aware
With tsMuxerGUi I open the .mpls file from the playlist folder (which contain the movie, this is very easy to know using HdBrStreamExtractor), remove all the audio and subtitles languages that I don't want, then, since I'm Portuguese, I add a .srt file with PT subs, choose the option "AVCHD disk" in tsMuxer, in the "Split & cut" tab choose "Split by size every... 4.000... GB" and click start muxing. After +/- 20 mins, you have a folder called AVCHD in the root of the external HDD containing the files with the movie, audio and subtitle tracks exactly the same as the original.
Of course, until the HDD is full, I have to "swap" the AVCHD folder from the folders I create for each movie, but when the HDD is full, using multiAVCHD 4.1, with very little effort and about 1h of compiling, I get a very nice menu with all the movies contained in that disk and no more need to "swap" the ACVHD folder, cause after all this is done you only get 1 AVCHD folder in the root of the disk, so, just connect the HDD to your PS3, in the XMB go to "Video", select your HDD with the "X" button and a single folder (called AVCHD) shows up. Just press "X" again and the PS3 "assumes" that is reading a physical BD disc, which can be quick seen by pressing the "triangle" button which shows the option when reading a real physical BD disc
I don't know if this information will be helpful or not, or even if it was already known by most PS3 users, either way, I decided so share it, just in case it will help somebody in the process of watching 100% quality BD movies in the PS3 without having much trouble.
Just to get a general idea, I have 17 500Gb external HDD's, with about 280 full BD50 movies, all with PT subs (99% of the movies don't have PT subs, but I just have to sync the time codes of the .srt file and add it to the muxing process). The time that takes, since I "unrar" the movie, until it's finished to be watched, is +/- 30 mins total.
Best regards to everyone.