How to suppress alert 'this app is not optimized for your Mac'
As mentioned (very briefly) in Apple's guide on how to Prepare your institution for iOS 12 or macOS Mojave, the CSUIDisable32BitWarnings property key can be used to disable the 32bit warning alert. 

This can be done in either of the following two ways:



In the terminal

According to this page, the warnings can be disabled by entering the following command in the terminal:

defaults write -g CSUIDisable32BitWarnings -boolean TRUE


To re-enable the warnings:

defaults delete -g CSUIDisable32BitWarnings


To display the current setting:

defaults read -g CSUIDisable32BitWarnings


where 1 means the alerts are disabled, and 0 or a does not exist error message means the alerts are active.



Using a management profile

The same effect can be achieved by preparing a management profile that sets the property key, as proposed by Apple in the above mentioned article. This may be the preferred solution to disable the alerts on multiple Macs.

This article explains how. It also provides a link to a sample management profile. The profile can be installed by downloading and double-clicking it.

For the sake of completeness, this is the example from the above link:

&lt;?xml version="1.0" encoding="UTF-8"?&gt;
&lt;!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd"&gt;
&lt;plist version="1.0"&gt;
&lt;dict&gt;
    &lt;key&gt;PayloadContent&lt;/key&gt;
    &lt;array&gt;
        &lt;dict&gt;
            &lt;key&gt;CSUIDisable32BitWarnings&lt;/key&gt;
            &lt;true/&gt;
            &lt;key&gt;PayloadDescription&lt;/key&gt;
            &lt;string&gt;Configures com.apple.coreservices.uiagent settings&lt;/string&gt;
            &lt;key&gt;PayloadDisplayName&lt;/key&gt;
            &lt;string&gt;com.apple.coreservices.uiagent&lt;/string&gt;
            &lt;key&gt;PayloadIdentifier&lt;/key&gt;
            &lt;string&gt;com.company.profile.57E80D89-1CA6-4386-8FDE-81DA0292CA3D.com.apple.coreservices.uiagent.FE123766-B72C-4620-9A21-CCABBEB48B2A&lt;/string&gt;
            &lt;key&gt;PayloadOrganization&lt;/key&gt;
            &lt;string&gt;&lt;/string&gt;
            &lt;key&gt;PayloadType&lt;/key&gt;
            &lt;string&gt;com.apple.coreservices.uiagent&lt;/string&gt;
            &lt;key&gt;PayloadUUID&lt;/key&gt;
            &lt;string&gt;FE123766-B72C-4620-9A21-CCABBEB48B2A&lt;/string&gt;
            &lt;key&gt;PayloadVersion&lt;/key&gt;
            &lt;integer&gt;1&lt;/integer&gt;
        &lt;/dict&gt;
    &lt;/array&gt;
    &lt;key&gt;PayloadDescription&lt;/key&gt;
    &lt;string&gt;Disable 32-bit application warnings&lt;/string&gt;
    &lt;key&gt;PayloadDisplayName&lt;/key&gt;
    &lt;string&gt;Disable 32-bit application warnings&lt;/string&gt;
    &lt;key&gt;PayloadIdentifier&lt;/key&gt;
    &lt;string&gt;com.company.profile.csuidisable32bitwarning.57E80D89-1CA6-4386-8FDE-81DA0292CA3D&lt;/string&gt;
    &lt;key&gt;PayloadOrganization&lt;/key&gt;
    &lt;string&gt;Company Name&lt;/string&gt;
    &lt;key&gt;PayloadScope&lt;/key&gt;
    &lt;string&gt;System&lt;/string&gt;
    &lt;key&gt;PayloadType&lt;/key&gt;
    &lt;string&gt;Configuration&lt;/string&gt;
    &lt;key&gt;PayloadUUID&lt;/key&gt;
    &lt;string&gt;57E80D89-1CA6-4386-8FDE-81DA0292CA3D&lt;/string&gt;
    &lt;key&gt;PayloadVersion&lt;/key&gt;
    &lt;integer&gt;1&lt;/integer&gt;
&lt;/dict&gt;
&lt;/plist&gt;




Update #1

This blog article might be interesting in this context: Mojave’s Legacy Software is doubly wrong



Update #2

File ~/Library/Preferences/com.apple.coreservices.uiagent.plist seems to maintain a list of alerts and last alert date for 32bit apps. If your alerts keep reappearing, it might help to delete it, but that is just an assumption.

rm ~/Library/Preferences/com.apple.coreservices.uiagent.plist