I've done what seems to be the expert consensus - I am not expert myself, fairly new player to DW, but read lots of posts - and here's my 2 cents:
a) if I do the 1 space port for ~3-4 systems approach (size of space port depending on planet pop and my cashflow) - with custom designed starbases or defense bases with just rec/med/commerce over rest of systems, then all is fine in terms of maintenance costs, and I don't really see any resource shortage except where I expect to - on systems I literally just colonized so of course there may be some shortage to insta-build a port/base.
However, the big, really big for me, negative is the inability to refit my local defense fleet I keep in each system on fleet posture defend-sector without exposing those covered systems to pirate attacks.
And somehow, the pirates always, always 'know' when I refit. The instant I pull a fleet out - either via automated suggestion popup or I manually control, either way- soon as fleet leaves to refit, pirates attack and kill whatever base I was still building, etc.
To some degree this can be moderated by staggering fleets manually to refit, but the logistics of that becomes sometimes more a nuisance than the hit the pirates do. The setting I really wish existed was refit all fleets vs refit all non-fleets whenever the suggestion to refit was asked. This way, at least my roaming defense forces would still be there, or vice versa my organized fleets when roamers are refitting.
I can also manually control 100% all refits, but again - by definition of an expansion empire, there will always be worlds uncovered - so only real way is to build 2 defense fleets per system, and manually refit only one at a time. But that gets to be bigger expense than just building a space port in every system, and much more a micromanagement nightmare as empire grows and how fast you tech up.
b) If I do the 1 spaceport in every SYSTEM (not world), with maybe a few systems that are so obviously close together I skip those, then I end up with ability to refit (and refuel with good amount of custom designed docking port designs) in every system. Pirates or AI can't really raid me and generally if a raid does happen during refit, ships are still waiting in queue to refit and at least part of the fleet can be sent to defend so basically, this option leaves me with effectively little to no 'uncovered systems' issue as above.
And to be honest, maybe because I am still playing on 'Normal' mode settings (for my empire, AI, and pirate numbers/strength) - I have not noticed any resource shortages just spamming spaceports on every 1 star system.
I DO notice maintenance costs being any issue, but I solve that by designing low cost small space ports for most worlds.
So of the two options, despite being as newbie player, I've decided to just stay with spaceport spam on every 1 star system with few exceptions when they are so close.
The refit exposure to me is a bigger nuisance than the possible resources being spread thin rather than stockpiled on key worlds.
Not sure, but maybe its because I use low cost small spaceports, but it seems the AI stores most what I need on my mega-spaceport homeworld anyways.