You can move a lot of your manufacturing and scientific capacity to other bases, and keep a tighter hoarding policy. Slavery is an easy way out for hoarders, but not the only way out. You WILL face choices in 'what to build'. Or, even more 'radical' solution, make an interception/loot base with nothing but crew quarters, hangars and stores.
Yeah, I find this is the most effective way to campaign in Piratez too. I do employ slavery, (love the option, actually), but understand that it is perfectly viable to avoid this. The key problem is that one single base is never really enough to effectively "do it all."
Your starter base is your HQ, and should be. Your best research facility is here, you can intercept from here, and can build up some manufacturing capability here.
My next bases are planned with global coverage in mind, and the first is placed to allow the airbus some more visibility in its limited range, before the Pachyderm allows me to place according to global activity as visible in the charts.
I tend to make that first base my recon base as well, building out hangars for Pigeons & Zepps for better coverage. I also build a second prison (for holding interesting captives I want to research/break later), and enough stores to hold my good back load of loot. I'll say this here too: I never use the large facilities (stores or barracks). The future single tile versions are far more efficient, and I'll just upgrade my normal vaults to armored vaults, and regular barracks to luxury barracks when the opportunity presents itself.
After my Stores/Recon base, I start working on building my first Manufacturing base. This gets more workshops and barracks as I have resources, and is mainly for financial support. Works on X-Grog, then Lingerie until I can get a Mint up, then counterfeiting becomes a full time operation here. It has the capacity to grind through ore hauls and loads of apples for faster cash if the materials are available, and also provides greater manufacturing that the HQ (which basically processes loot and makes battlefield equipment like weapons, ammo and armor) to do some special runs of equipment production. This is also a good place to build craft (so it needs a hangar too).
About the same time I get a grog line up in the Manufacturing base, I start my Lab base. This can start with just a library and a single brainer. I put in a prison or two and it becomes my main interrogation base. There is some micro to move prisoners from the intercept base, but that base has higher brainer capacity and can work on figuring out all the stuff we've captured. I build this base up as resources allow, with Study Rooms being a key tech to allow me to start plopping down facilities for 2 brainers at a time. I like early combinations of 4 brainers assigned to research projects as it feels pretty efficient. Later techs become more demanding and I assign 10 or more at time for more difficult techs. Eventually this base can outstrip the HQ in research capacity (as in my current campaign, 1.3 years in, I have 20 in my Lab base, and 17 at the HQ).
I've also taken to dedicating a base to crew training as Meridian has done in his series. This is a great second intercept base for keeping the Pachyderm around once you get the Bonny up, if you so desire. I feel like 20-40 hands here is a good reserve, and start building out this capacity when Dojos and Voodoo schools start becoming available. I'll rotate wounded troops out to here when they have long recovery times, and otherwise use this to screen Voodoo, and train rookies into Vets.
All of this is solid infrastructure for the mid-game, but for the end-game, One more base needs to be set up: The Industrial Base designed to handle construction of the Conqueror. This is will become a huge cash cow when Defense Contracting becomes a thing, and we'll just churn out Battle Tanks and fuel cells while waiting to get all the keys necessary.
Because of the huge Plastasteel and Hellerium requirements of some of these end game items, converting one or two of the last recon bases into huge storage networks has a certain amount of appeal. I've not played the endgame, so I don't know how often these might be lost in Crackdowns, and how crippling their losses might be. The cost-benefit of multiple shrouds becomes an interesting question in these instances.
Edit: Blarg. Just realized I was thinking I was writing this in the main PirateZ thread. It kinda feels off topic here. Sorry bout that.