The introduction of delayed spending doesn't exist in SINS right now. When you queue up orders, there is no ambiguity as to what you want to pay for, when you want to pay for it, and where you want to spend it. Auto replenishment means ceding at least some control to the game to make some of these decisions for you.
Possible issues to consider:
1. What happens if you don't have the resources to order a build of the replacement ship at the time it is destroyed? It can't be added to a build queue since all ships in a build queue are paid for. If we allow unpaid ships into a build queue, then when does it get paid for? (Allowing unpaid ships into a build queue would dramatically alter the character and strategy of the game. Once you have that, the argument can be made that you should be allowed to queue builds any time you want even if you don't have the resources since they will start building once you do have the resources. A change like that would dramatically alter the game's current dynamics. It might work, but I don't think you intended a change to such a fundamental aspect of the game.)
2. Where do the build orders for the replacements get queued up? Assuming that the game implements some type of automatic build location optimization algorithm that takes distance, time to build, and other factors into consideration, does the player have any ability to influence those decisions? For example, can I tell it to calculate pathing costs based on a rule that the newly built ship(s) must stay in friendly territory until the last jump needed to join with the main fleet? Can I specify if path costs should include projected orbital motion? (For short build queues, orbital motion may not matter much, but if we are auto-building very long queues, then orbital motion becomes more of a concern.)
3. Do build locations get re-optimized if the player builds additional factories that didn't exist at the time the original ship to be replaced was destroyed? (This could happen if enough ships are destroyed to create sufficiently long build queues for a factory to get built in less time than is required to finish building all of the replacement craft.) What about if one of the factories building replacements is destroyed? Do the ships get re-allocated to other factories that are still operational? If so, do the reallocated build requests move to the end of the line, or does the order get shuffled to try to maintain the same overall order of build as the ships they are being built to replace were destroyed in?
4. How do auto-generated build queue orders interact with player decisions if they click on one of the factories building auto-replacements? For example, if the player cancels the build of a replacement ship at a specific factory, does that mean that they are removing that ship from the blue print, or should the game simply assume that means that it needs to auto-pick a different factory for the build of that specific ship?
I could keep bringing up other potentially unintended consequences of this change, but after having given it some thought, I think I have a potential solution that is in keeping with the current SINS philosophy/style. The simplest solution I see that avoids most of the unintended consequences is to allow a fleet composition to be specified, and provide a button called something like "Replenish Group" that will show the cost to build all of the ships that are needed to fill in anything that is missing compared to the target configuration. It would also allow you to choose which gravity wells with available factories should be used for a replenishment. If you have the money (and the supply) to build everything needed to reach your target configuration, then you can click the button. Otherwise, you have to change your target to something that fits within the constraints before you can click the button. (Factory types at the participating gravity wells would be taken into consideration as well to determine if you can click to replenish.)
With this solution, resources are decremented at the time the user clicks to spend them, so there are no unintended consequences due to automated spending concerns. This also leaves the player very much in control of what will be built, and where it will be built, so very little is ceded in terms of control. Basically, to me, this feels more like the natural way for a SINS game to eliminate the where's Waldo tedium brought up at the beginning of this thread.