Maybe it isn't a cider problem, I'm having a similar issue with lein.  
Working in the project directory created by lein:

$ lein repl
nREPL server started on port 42585 on host 127.0.0.1 - 
nrepl://127.0.0.1:42585
REPL-y 0.3.7, nREPL 0.2.12
Clojure 1.9.0
OpenJDK 64-Bit Server VM 1.8.0_151-8u151-b12-0ubuntu0.16.04.2-b12
    Docs: (doc function-name-here)
          (find-doc "part-of-name-here")
  Source: (source function-name-here)
 Javadoc: (javadoc java-object-or-class-here)
    Exit: Control+D or (exit) or (quit)
 Results: Stored in vars *1, *2, *3, an exception in *e

user=> (use 'foobar.core)
nil
user=> (math/expt 2 3)

CompilerException java.lang.RuntimeException: No such namespace: math, 
compiling:(/tmp/form-init2355284152590406554.clj:1:1) 
user=> 


It seems that the lein repl also is not processing the 

 (:require [clojure.math.numeric-tower :as math])

line in project.clj.

On the other hand:

user=> (require 'clojure.math.numeric-tower)
nil
user=> (clojure.math.numeric-tower/expt 2 3)
8


On Friday, January 19, 2018 at 12:10:59 PM UTC-5, Sean Corfield wrote:
>
> Can’t reproduce in Boot either. Based on that CIDER ticket, it may be 
> something specific to Andrew’s project.clj file…
>
>  
>
> (! 910)-> boot -d org.clojure/math.numeric-tower repl
>
> Retrieving maven-metadata.xml from https://repo1.maven.org/maven2/ (1k)
>
> Retrieving math.numeric-tower-0.0.4.pom from 
> https://repo1.maven.org/maven2/ (1k)
>
> Retrieving math.numeric-tower-0.0.4.jar from 
> https://repo1.maven.org/maven2/ (5k)
>
> …
>
> boot.user=> (clojure-version)
>
> "1.9.0"
>
> boot.user=> (require '[clojure.math.numeric-tower :as math])
>
> nil
>
> boot.user=>
>
>  
>
> Sean Corfield -- (970) FOR-SEAN -- (904) 302-SEAN
> An Architect's View -- http://corfield.org/
>
> "If you're not annoying somebody, you're not really alive."
> -- Margaret Atwood
>
>  
> ------------------------------
> *From:* clo...@googlegroups.com <javascript:> <clo...@googlegroups.com 
> <javascript:>> on behalf of Alex Miller <al...@puredanger.com 
> <javascript:>>
> *Sent:* Friday, January 19, 2018 6:04:42 AM
> *To:* Clojure
> *Subject:* Re: numeric-tower versus clojure 1.9 
>  
> I can't reproduce this problem in either a lein repl or clj repl using 
> math.numeric-tower + clojure 1.9. Looking at the code, I don't see anything 
> that should be different with Clojure 1.9.
>
> On Friday, January 19, 2018 at 7:38:57 AM UTC-6, Bozhidar Batsov wrote: 
>>
>> I also got a CIDER ticket about pretty much the same problem 
>> https://github.com/clojure-emacs/cider/issues/2169 
>>
>> I guess there's some problem with Clojure 1.9 and the tower, but I'm not 
>> sure about its exact extent. 
>>
>> On 18 January 2018 at 02:41, Alex Miller <al...@puredanger.com 
>> <javascript:>> wrote:
>>
>>> I can't reproduce that locally. Checking with the new clojure 1.9 clj 
>>> tool: 
>>>
>>> $ echo '{:deps {org.clojure/math.numeric-tower {:mvn/version "0.0.4"}}}' 
>>> > deps.edn
>>> $ clj
>>> Clojure 1.9.0
>>> user=> (require '[clojure.math.numeric-tower :as n])
>>> nil
>>> user=> (dir n)
>>> MathFunctions
>>> abs
>>> ceil
>>> ...
>>>
>>>
>>> On Wednesday, January 17, 2018 at 4:26:44 PM UTC-6, Andrew Dabrowski 
>>> wrote: 
>>>>
>>>> Is clojure.math.numeric-tower incompatible with clojure 1.9?  The 
>>>> numeric tower is still at version 0.0.4, 4 years old.  WHen I try to use I 
>>>> get the error
>>>>
>>>> 1. Caused by java.io.FileNotFoundException
>>>>    Could not locate clojure/math/numeric_tower__init.class or
>>>>    clojure/math/numeric_tower.clj on classpath. Please check that
>>>>    namespaces with dashes use underscores in the Clojure file name.
>>>>
>>>> In particular math.numeric-tower does not seem to obey the 
>>>> dash->underscore convention, nor does the installation seem to include 
>>>> init.class or .clj files.
>>>>
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>>
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