There is no right or wrong, some people like a mess, others like it clean. I suspect that over time with expercience, one starts to optimize/compact flows.
I have a single flow that is taking many steps and it's all connected via link nodes just to make it a bit more compact within the group/layout. I wish there was a collapsible group though (with its own variables).
I don't have nearly such large flows as that.
Instead I put any self-contained processes on a separate editor tab and use link calls to connect to it.
Examples include database insert/select, email or SMS notifications etc.
No doubt other people prefer subflows for such tasks.
I also put the nodes which perform a defined function into a group together.
I try to line up nodes vertically and horizontally.
Within the group I use junctions to prevent wires crossing and passing beneath nodes.
Connections from one group to another mostly use link calls.
Like this it's easier for me to identify the flow and nodes to update when I need to modify a program.
What is the difference between junction and link nodes?
I sort of agree with your second picture, but shall accept that when designing something my flows look like that sometimes.
Interestingly I am turning to the thinking that within a group (block) I won't use link nodes.
The only link nodes are the main input or output of that group.
Your screenshots are how I work too. The second one would only be used to determine how to get something to work and lay it out correctly.
This is one example of how I use the link nodes.
This group is just to display a nice interface on the dashboard for controlling one of my wireless speakers.
Top input is from my music flow that formats a msg object.
Bottom input is for enable/disable of the controls when performing long actions (skip album/artist)
Output is for change in volume, track or play/pause control.
I format it this way, so that I just need to copy/paste the entire group for a new speaker and change a couple of things. Very modular.
after getting more tips and experience from the forum, this is what my newer flow looks like, grouping them and connecting with link nodes, does appear better.