Electronic – Some LTspice questions. Decoupling capacitor doesn’t effectively block DC. Pull up resistor voltage doesn’t drop to logic low level

The best way to do this would be to use a transistor as a comparator to make the transition sharp.
Here is an example circuit:

It uses the LDR as the upper part of a voltage divider. When the LDR resistance drops the voltage at the transistor base rises and turns it on. The transistor can be any general purpose NPN.
We can calculate the resistor value based on whereabouts we want the turn on to happen.

Let's say the LDR resistances goes from 200Ω (dark) to 10kΩ (dark). We want the transistor to turn on when the LDR is at 5kΩ. The supply (V+) is at 3.3V. A typical NPN transistor turns on at around 0.7V, so if we do:

5,000 * (0.7 / 3.3) = 1060Ω needed for the base resistor. We can pick a 1kΩ resistor since it's near enough. Adjust your values to suit your turn on point.

Here is a simulation of the circuit:

The horizontal axis is the LDR resistance, and the blue line is the voltage at the Vout point (You connect this to the Rpi input pin - must be set to input. You can add a 1kΩ resistor between Vout and the Rpi pin to protect it in case of accidentally setting it to output) We can see the transistor turns on at around 5kΩ as predicted (won't be exact as the transistor base-emitter voltage will vary with temperature, etc but near enough for your purposes)

Note that the transistor output is low when it's light and high when it's dark, you can swap the LDR and resistor around and use 5,000 * (3.3 / 0.7) = 23.5kΩ for the resistor if you want it the other way round - this is actually a better configuration as it draws less current (due to higher resistances) so if that's important use this version.

Pull-up and Pull-downs are normally used to ensure a line has a defined state while not actively driven. They are used on inputs to prevent floating lines, rapidly switching between high and low and a middle "undefined" region. Outputs normally do not need them.

But most mcu pins are GPIO, and sometimes on startup are defined as inputs instead of outputs. As you said, sometimes you don't want an IC pin input floating on startup, especially like a reset pin that you would normally drive with your microcontroller's GPIO.

This is when you use a Weak Pull-up or Pull-down on the line. Because they are weak, and you choose the default state, they provide no interference with your circuit (If the input is supposed to be low at all times, then pulled high, you choose a weak pull-down, and vis versa), but they do consume a bit of current. This is why you choose a resistor weak (Higher the value, the weaker) enough for the job.

Another normal output setup that uses pull-ups (or pull-downs, rarer) is Open Drain or Open Collector connections. These only drive a connection low, or release the line, leaving it floating. The pull-ups are used to bring the line to a high logic state.