Magento 1.9 – Fix Meta Keyword Tag Not Showing in Browser Source

This is a business question, probably not the best forum to place it, although we don't have an alternative for you. There two approaches to SEO, the business (qualitative - artistic) and the technical (quantitative - technology). SEO services and most sites will use majority business and minority technology, the technical approach is the opposite.

This is where it becomes important, the top 5% of retailers generate 50% of all online revenue, the top 1% generate 80% of that. Now, either business -or- technical can, with a lot of experience, time, and determination achieve 80-95% exposure, however you are still fighting for 50% of the revenue.

The top enterprise companies combine both technical and business together to get in to the top 5%, the top 1% improve with higher efficiency, trust, product count, (we use scaled tier 1/2 technology for the top 5% & top 1%).

Bringing it all together the meta description is good to have - be it automated from the description in code (140chars max) or manually entered, the other two are basically irrelevant. The problem is that it is just a drop in the ocean. On the business side you need high product counts, not using canonicals (it confuses everything), actual changing written content, social media, etc. On the technical side you need hosting, tier 1/2 is 2x less effort to rank that tier 3/4 (Nexcess) and 2x less effort than tier 5/6 (optimised Magento hosts) and 2x less effort that tier 7 (mass hosts) - you still need 1-2s dynamic page loads (no fpc).

To point you in the right direction, remove the categories in the product urls and add a 1-2 keyword prefix to the product. The other factor is that 70% of Google's revenue is generated by Adwords, they are not going to make it easy.

You will find everyone is now starting to jump on this as Google are making it harder to rank (revenue), there is more competition in Adwords therefore they are becoming less effective by the month, and everything is moving towards trust (enterprise sites) - so unless you are either very very niche or look like a large enterprise (hence why we use scaled hosting from Large Enterprise consultants) - you will end spending 8% of revenue on marketing compared to Amazon.com's 4%.

Based on the technical side most sites will take months to reindex, so what happens is people make a change, wait a few weeks, see no difference and make another change. By the time their change has been indexed there are multiple other factors in play and they never know what works and what doesn't. At around 30,000 products on top tier hosting is the breakeven where you can let the site just run and it will generate revenue, below that you need to increase your business methods to offset the lack of content (the wonders of onboarding tools).

Now, why can't everyone use tier 1/2 hosting or tier 3/4 (Nexcess clusters), well it is much slower than the lower tier hosts, so you need to pay more for the same result. So you are then balancing the cost of the hosting and architecture against the cost of your time to rank via business methods. Again, we bypass this as some consultants found a way to combine the two so we use their hosting.

It not what you want to hear, but as they say, knowledge is power.

This is not an answer to your question, but it may be a solution to your problem.
You don't need to disable the head.phtml in your custom module pages. There might be useful information in there that you would want in your pages.
In order to change the meta data you can do this.

If the meta values are always the same you can use the layout xml.

<page_handle_here><!-- your page handle module_controller_action -->
    <reference name="head">
        <action method="setTitle" translate="title"><title>Your meta title here</title></action>
        <action method="setKeywords" translate="keywords"><keywords>Your meta keywords here</keywords></action>
        <action method="setDescription" translate="description"><description>Your meta description here</description></action>
    </reference>
</page_handle_here>

If your values are dynamic you can use this in the action of your page after calling loadLayout

$head = $this->getLayout()->getBlock('head');
if ($head) {
    $head->setTitle('your title here');
    $head->setDescription('your description here');
    $head->setKeywords('your keywords here');
}