Strike craft upgrades, in my opinion, should only be used in uncolonizable gravity wells, especially as Advent. Spend tactical slots on cheap hangers, not starbase upgrades on expensive strike craft bays. Only use them in wells where you cannot build hangers. If you need mines, use your drone hosts as mine-layers.
Typically you should use either disorient or meteor, not both. An intelligent player probably won't even attempt to rush your starbase if you have one or the other, and will instead attempt to barrage it from a safe distance. This leaves these upgrades more as deterrents to keep the enemy away from the starbase. Personally once I have meteors I don't invest (heavily) in weapons upgrades for this very reason; an enemy is likely to keep his distance and not come into range of those weapons.
Unless I'm in a very late-game scenario where money is no object, I will very rarely fully upgrade starbases. It's throwing all your eggs in one basket, which can be disasterous if the thing is destroyed or the enemy fleet bypasses it. You should buy upgrades because the starbase needs the utility to fulfill the role you intend for it, not because the starbase still has room for improvement.