I'm also very wary of riddles in RPGs. They generally make great sense to the GM but just frustrate players. However, you do look like you have it covered through knowledge (or Logic?) rolls... If my character has a logic/intuition of 6, he's going to solve a lot more riddles than I, the player, ever will.
Background information on the site would be important, as the characters will probably look into it via Legwork, unless you are saying that the Altar is literally just something they stumble on and not part of the actual job they are hired for, in which case, be wary of the team just avoiding it outright (maybe not, depending on the players, but most of my characters will avoid dangers not associated with the job at hand). But fleshing out the background could be great for future stories, if not so much for the run they are on in the moment. Handwavey plot devices are fine for one off runs.
Anyhow, it looks like the story here is something like:
Get job to find reagents.
Head to the woods.
Eventually have to fight a Spirit of varying power depending on how well they solve a riddle.
Return to talismonger.
Get Paid.
If your players are generally new to Shadowrun and this is just run #4 or 5 (which it seems like, after 15 Karma), then it sounds fine. If the players are a bit more experienced, they might want a bit more to it. Going berry picking and running across a bear isn't, to me, a Shadowrun... as a player, I'd probably not be very engaged with the story.
Consider making the Altar actually part of the job. Maybe there's a focus there that the Johnson wants (probably why he isn't hiring a team with a mage). Fleshing out the details can indeed make it more exciting. Also, if there is an actual magical altar, their legwork might be used to actually teach them more about how magical threats work, etc.