Or do I need to check the second option to connect to nodes that are running as a hidden service?
Is there a benefit of checking both options?
As far as I know, no. The first option of routing everything through Tor implies the second option. Because the second option mainly exists so that you don't have download all block and transaction data from nodes on the clearnet using Tor, while simultaneously being able to download from nodes that are only accessible via Tor.
in the past (several years back), there was a bug in Bitcoin Core related to the Socks5 proxy options... I forget the details, but using the "separate socks proxy for Tor connections" was causing a problem IIRC
if you're only connecting via Tor, then using the separate Tor-only socks proxy isn't necessary, you can set only the socks proxy and it will work fine. The separate socks proxy for Tor-only is only necessary if you are running 2 proxies simultaneously, one for for Tor and another for a proxy to some other alternate network routing. I expect most people are only using a Tor proxy as their alternate (or only) network, so the second Tor-only setting is not needed.
In future (i.e. probably Bitcoin 22.0), using both proxy settings may become more common, as I2P support is coming in that release. I think the CJDNS protocol is already supported in 0.21.0, as all it requires is already in the new address format that comes with Bitcoin 0.21.0, not 100% sure on that however