I would say it would be best to allow the player to choose when to make these changes to their fleet, but the changes still take time depending on the extent of the changes, and whether or not the given resources to do said changes are at hand.
Your fleet yard and support infrastructure would then determine how long major changes actually take to do, your industry centres and infrastructure determine how long it takes to actually produce your weapons/armour, and finally your logistical centres and storage determine whether or not you can keep suitable stock piles for a number of weapon/armour types on hand at any given time.
Investment in your logistical/storage ability means that you can stockpile various styles of weapons and ammunition, which when combined with a properly sized fleet yard and support infrastructure you have the ability to field what would normally be a horribly tiny fleet for general defence, assuming you keep up on your intelligence gathering ability. You don't need a massive fleet on hand all the time that is ready to defend against "anything", because you look at what is coming your way and then perfectly tailor your ships to defeat it in a highly efficient manner.
Cylons have a fleet coming at you? Load up the EMP missiles and basic nukes. After you've killed off that fleet, return to the shipyard and load up the biological weapons to knock down that incoming Zerg like thing heading your way.
Or maybe you rather invest less in stockpiling or fleet yards, and invest insane amounts into your general industry. Embrace Just-In-Time delivery. Wear your opponents down and produce new and terrifying weapons faster than their intelligence geeks can process reports for their spies.
Want a missile heavy force? Well you can change out warheads for a fraction of the time and effort to address a new threat, but you're going to need a steady flow of them to the front lines. Contrast that to your beam weapon fleet, which uses barely any munitions resources while in combat, but takes a week at the fleet yard rather than a day to refit and change the ship's weapon effects.
Do you build your ships with a generalized hard-point system so you can reduce your refit time requirements? Or do you go with internal weapons mounts buried under massive armour where they're far harder to destroy?