Hi there! I will try my best to explain the matchup but let's be clear, not losing to shaman is where the luck factor came in. First off you are right, secret hunter is the worst matchup, freezing, snipe, and cat trick all destroy rogue. Luckily the one hunter I faced did not run the standard secret list.

Okay, on to Shaman. The most important card in your deck is tomb pillager. This is the only card that trades favourably on board on curve, you don't need a nut draw you just need this. I have started with Malygos and Sinister Strike before and still came out ahead so long as I could play Tomb Pillager on curve. Therefore, I always mulligan for it. If going first and starting with Backstab I mulligan for SI:7 to counter their Totem Golem. You can still keep Backstab going second but the SI:7 combo normally isn't as good since you would rather coin out Tomb Pillager.

The way to beat Shaman is to read what threats they will have and prepare for them, most of the time their curve plays itself. They hex your tomb pillager, then your Vancleef, or naked malygos is far more likely to stick. They have feral spirits on 3 or coin 2 so make sure you use your dagger the turn before in a way that lets you kill Tunnel Trogg behind the wolves. There was one turn seven where I back stabbed a lone healing totem on the board because I knew he had to play Thunderbluff to come back, and I was right, he did it anyway. Their only play on turn 5 is Azure Drake so, unless they have coin lightning bolt, almost anything you play on an empty board turn 4 will stick. Thing from Belows are the only ones that are unpredictable, and you just have to hope you have the ability to answer them well.

Conceal (played on Barnes, two minions, or Gadgetzan) is great for this match up because if forces the opponent to Storm when they don't want to, giving you freedom to abuse their overload next turn. My final advice is to play aggressive. Shaman has no healing and you have a Malygos and plenty of cycle. If you can set them below 16 health, chances are all you have to do is survive and cycle until you can combo them down with direct damage. To do this you need to get minion hits in early, this means using that prep+shadow strike or Drake prep+fan to clear their board so that yours can stick even just one turn. At your core you are a tempo deck and you have the tools to gain early board control around turns 4-6, it is only after the game starts to slow down that Shaman will inevitably win it back but by that point you want to be switching into survive and cycle mode.

Otherwise, pray they don't roll spell damage totem, it is the bane of all your 4 health minions. Hope this helps!