Yeah and? I don't see where any of that says that Cruisers don't mount
missles or disruptor torpedoes. Frigates mount them too and just
because it isn't their main weapon doesn't mean they don't pack them,
they had two "gun" mounts at the front of the cruisers to begin with,
and even if they came out of the same tube there is nothing to prevent
that, I mean the Sheridan tank could fire missles out of its gun back
in the 70s. The game shows them firing them, so I am pretty sure
Cruisers can and do fire missles.
Some newer Alliance vessels mount Javelin for extreme close range engagements, but they are not fired from railguns. And for good reason:

This is a Javelin missile. Railguns don't have a diameter greater than the width of their projectile, and the largest railguns in the alliance military fire 20 KG iron slugs that you can fit in your hands (assuming you're strong enough to lift them).
The reason they fire missiles in the cutscene is because the cutscene department didn't know what exactly the combat was supposed to be like, and started working on it. By the time the departments coordinated and realized the mistake, it was too late. This is why most of the ships fire missiles and only very occasionally fire slugs.
This is also the reason that in the cutscene, there are no Council vessels near the Citadel relay, even though the game explicitly states that the council has its fleet on active guard duty to defend the relay because they knew he might be coming.
The "cruisers" in the custcene were using the model and textures of the dreadnought, but they accidentally put like 20 of them in the frame when the Human alliance is only supposed to have 6 with 1 under construction, and so Bioware rebranded them cruisers.
As for Nukes, it is evident they are obsolete, why use an extremely
expensive and easy to destroy object when you can hit it with a couple
massively powerful chunks of metal in a matter of seconds? We have
never seen a Dreadnought fire on a Reaper with its main gun, much less
a fleet of them.
Sure is a good thing the Destiny ascension isn't a dreadnought that shames the main gun on any alliance vessel and was participating in the battle of the citadel. Otherwise the point you just made would be very wrong.
Why nukes? Because you can fire missiles from several light-seconds away, which is far beyond the effective combat range of any main gun, even a reaper. The main guns of dreadnoughts are
not powerful enough to penetrate their kinetic barriers, even the Destiny Ascension. Are you implying that there was not one single dreadnought in the battle of the citadel?
Even if they were powerful enough to do that, nukes would still be awesome because they are small enough to be frigate or fighter mounted, but still powerful enough to destroy a huge capital ship.
Then since they're operating under their own power, they can easily accelerate to high relativistic velocities to bypass point defense then slam into their targets. Blamo. Shabams.
And the codex is contradicted by dialogue and plot. There is the issue
of the derelict Reaper's mass effect field protecting it from the
turbulence around the brown dwarf and the Collector base's mass effect
field being able to protect it from the radiation and various other
effects of the being in the galactic core.
1. No, the codex is contradicted by gameplay mechanics. Nothing about the plot or dialogue contradicts it. In fact, the entry on body armor says that armor is hardened against radiation, extreme heat and so on. All we have in dialogue is "its frying our shields", which is easily and parsimoniously explained as "it's heating up the emmiters".
2. The mass effect fields are preventing it from falling into the star, not preventing it from being burned or anything like that. The radiation of the star at that distance was not enough to do significant damage, and the hull of the reaper is in-tact.
3. The collector's base is not stated to be protected from radiation by mass effect fields. It exists within the "safe zone", the method by which it is protected is unknown.
As I mentioned before, nuclear missiles, or missiles of any kind, are vulerable to ECM's and point defense systems.
GARDIAN point defense is limited to lightspeed. If you got a Kodiak shuttle (which can go FTL) and loaded a nuke into the bay that houses passengers, it would breeze past point defense before they even knew it had been launched, and would detonate when it gets there.
As for timers, space battles occur at much greater distances. We are
talking about at least millions of kilometers. The margin of error is
going to be much larger.
Yes, they do take place at those distances, but priming and ignition of a fission-fusion bomb takes place in less than a second. You're making a mountain out of a molehill.
The reapers are approaching from what we can assume is deep space, so i
say, why not shoot them with the mass relays? you could shoot nukes,
small moons, ships filled with explosives ect. from mass relays in the
direction of the reapers, and, since there is no friction in space,
they will keep going quite fast (you can jump halfway across the galaxy
in seconds) until it hits someone. Just an idea.
Commander Shepard and TIM didn't see the last frames of Mass Effect 2. The audience did. We have no idea where they're coming from, or even which direction, or how close they are. There's no way they could know where to aim.