Strangely enough, Runer112 in the shoutbox just reported a similar problem earlier, but with a different calculator line (TI-8x series).

[20:31:30]   Runer112   hey guys
[20:31:40]   Runer112   I think overclocking my calc is making it slower
[20:32:14]   Runer112   CPU frequency is inversely proportional to speed, right?

I wonder if it could be some emulator bug, though, in your case, causing it to adjust the speed down based on your CPU speed in order to keep games from running too fast, but inadvertently causes them to actually run slower?

Mine runs faster when overclocked.

I noticed this when I downloaded Crafti onto my calc and it ran a lot slower than it did in the picture.

That's only because it's running in nspire_emu. On a real nspire there are some other things affecting speed, e.g.:
- caches
- RAM wait states/speed
- Pipeline stalls
- touchpad and keypad (I2C for the touchpad is slow)

they aren't emulated accurately enough to behave just like the hardware but it depends on which software is being run.
Especially crafti, which depends on memory speed mostly, is very much affected by this.

Sorry if I was a bit ambiguous, but I was asking if overclocking would slow your calc down in the long term.

If you can't notice any difference after overclocking, it's better for just a single reason: Saving battery charge!
Higher speed means more power comsumption, basically. There's no other disadvantage to it.
But DO NEVER, EVER increase your AHB frequency further than 66 MHz! You may corrupt some important data which cannot be restored afterwards and your calc could be bricked forever.

The higher loading times you experienced could be some other clock (e.g. SDRAM, I don't know what clocks are connected to which peripheral in the nspire) still at a lower speed.
If the RAM was fast enough to load a word in four CPU cycles, it may be ten now.
Or you have a lot of files on your calculator which slows down file access a lot. If it takes very long to open the document browser (after bootup, not standby), backup the important files and format the partition using the maintenance menu.

Just out of curiosity, if the CPU could run at a much higher speed, why didn't ARM set the speed higher?

TI wanted to have a higher battery life time and little power consumption.

Everything file that I have is 16MB or less, so flash memory performance shouldn't be too big of an issue when actually playing a game.

The flash is incredibly slow. Really slow. The RAM speed can be compared to computer HDD speeds and the flash to a below average-speed DSL connection.
At least that's what linux told me, but it feels like it's the sad truth 

(it takes like 15-20 seconds to load 69MB, so about 4MB/s and an average hdd is like 10MB/s or something?)

It takes 10 seconds for me to load 5 MB, so about 500kB/s...
An average HDD is about 90MB/s, but there are much faster ones.

By the way, what does the base frequency do?

The base frequency isn't used by anything directly, there are some dividers to get the cpu clock from it and then some dividers to get the AHB clock from the CPU clock.