I am really conflicted about this, as I know I could not find such great and affordable apartment in Zurich.
I am currently looking to buy an apartment. I found one that is perfect for me but it is quite far away in Neuhausen am Rheinfall. Still, what is tempting is that I will be 2 minutes from train station, from where I can take the s-bahn to zurich. I currently work in Altstetten (when not from home). Commute would be 1:15 minutes (a lot). If I would work in Oerlikon it would be around 50 minutes which could be acceptable.
One hour is nothing, take it. At the end, you can always work from home or change your job
Property in canton ZH will be more expensive than in SH. The Neuhausen/SH is great in general for free time activities, cross-border shopping etc.
And the commute to ZH is not such a big thing. There are people who commute daily from Singen to ZH HB and further.
The connections between SH and ZH are normally excellent.