Are tones sometimes glossed over? To elaborate, although ni3 hao3 has a double third tone, when I hear native speakers say it, it's said so quickly that they definitely are not using that tone, nor is there feasibly time to use the third tone when it's said that quickly; I mean there isn't time to lower and then raise pitch when the syllables are practically spat out.

So the question is whether tones are sometimes, to some extent, omitted? Especially in extremely common phrases like ni hao?

Listening to native pronunciation clips on many sites (for example, one among many: http://www.learnchineseez.com/lessons/mandarin/pinyin/index.html), take for example the clip of wǒ hěn hǎo. To my uneducated ear, none of those syllables have a full third tone pronounced on them, especially "hen3." It just sounds like no tone.
There is a very interesting phenomenon in Chinese, called 语音变调（tone sandhi).

Here are the rules. (Note: all the rules apply only characters in the same word/phrase)

Tone Rule #1: 3-3 to 2-3

When there are 2 third tones in a row in the same word/phrase, the first one becomes second tone. This rule is always followed automatically, even though it will not be reflected in the pinyin.

The reason of this tone sandhi, I personaly believe, is because 3rd tone needs a little bit more time to pronounce than any other tones, and if multiple 3rd tones roll in a row, a lot extra time will be needed if pronounce them all in 3rd tone, and that will break down the speech fluency. So in order to keep the speech speed nomal and speak natually and fluently, we drop the lowering part of the 3rd tone, and just keep the rising part, which makes it 2nd tone.


  Like 你好，很好，买米，好酒，土改，检举，冷水，and many more.


Note this rule doesn't apply if the two third-tone characters in a row are not in the same word. 


  For example: 中午我出去吃饭。午 and 我 both are still 3rd tone in normal speed, and there will be a very short gap between 午 and 我. But when speak very fast, again 午 will become 2nd tone.


When 3 third tones in a row in the same word/phrase, both 1st and 2nd character will have 2nd tone. 


  For example: 你好早啊。Tone pattern is: 2-2-3. This is a greeting used in the morning, used to the peope who arrive before you.


When 4 third tones in a row in the same word/phrase, the tone pattern is: 2-3-2-3. like 剿匪手本。

When 5 third tones in a row in the same word/phrase: 2-3-2-2-3. Like 剿匪手本好.

When 6 third tones in a row in the same word/phrase: 2-3-2-3-2-3. Like 剿匪手本挺好.

Tone Rule #2: 不

When the word 不 (bù) precedes a fourth tone, 不 changes to second tone (bú). This rule is always followed, automatically, even though it will not be reflected in the pinyin.


  Like 不对，不去，不错，不坏，and many more.


Tone Rule #3: 一

3.1 The character 一 (yī), meaning "one," is first tone when alone, or at the end of a word.


  Like 一，第一，始终如一。


3.2 It becomes second tone when followed by a fourth tone。 


  Like 一个 (yí gè) 一次 (yí cì) 一寸(yí cùn) 一夜(yí yè) 


But This rule is NOT always followed, for example, 一月一号(Jan 1), some people say yí yuè yí hào, but others say yī yuè yī hào. 

3.3 It becomes fourth tone when followed by any other tone. 


  Like 一斤(yì jīn) 一天(yì tiān) 一杯(yì bēi) 一般 (yì bān) 一些 (yì xiē) 一直 (yì zhí) 一条 (yì tiáo) 一起 (yì qǐ) 一点 (yì diǎn)


But This rule is NOT always followed, for example, (第)一期工程, it is (第)yī qī 工程, not (第)yì qī工程. Another example: 一条, when used in Mahjong for "one stick" tile, it should be pronounced as yī tiáo, not yì tiáo. Some people say 一鸡 (yī jī) for "one stick" tile. 

3.4 It becomes a Neutral Tone when in the pattern of X一X.


  Like 听一听 (tīng yi tīng) 看一看 (kàn yi kàn) 走一走 (zǒu yi zǒu) 等一等 (děng yi děng)


The last but not least, DO NOT TRY TO REMEBMER ALL THESE RULES. You just need to listen to native speakers and imitate, until it becomes your natural speaking habit.